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From: Julian U. <jul...@ru...> - 2025-12-03 08:10:19
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Hi all, At EuBIC-MS (eubic-ms.org), we have found that there might be a lack of in-depth educational resources about computational mass spectrometry. One way to address this issue, would be to set up a community-driven online open textbook. With that in mind, we would like to hear from you and seek advice on the format, its contents - or whether such a resource is needed at all. Please fill in the form below before 31 January 2026. It should only take two minutes. https://forms.gle/GPvTjsUSwyfNRkvg7 Best regards and thanks, Julian |
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From: Lee S P. <lee...@gm...> - 2025-05-01 21:53:53
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Hello I downloaded knime and the current openms nodes and have been working on building my first workflow in several years. DecoyDatabase has been throwing an error that I can't seem to solve. StdErr shows: " Parameter settings are invalid. Both 'in_relevant_proteins' and 'out_relevant' must be set or unset. " However I don't see these under parameters or flow variables. I've been using a swissprot fasta DB as my input, which works fine for the search engines I'm using in my workflow, I want to use DecoyDatabase to build a decoy set from this. Thank you! Lee |
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From: Mike H. <Mik...@in...> - 2025-02-05 20:18:42
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Hi OpenMS, We tried modifying our RNA sequence with * to indicate phosphorothioate modifications with and without brackets. Also, we did not see phosphorothioate as a modification within the modification list. Can you help us by letting us know how to search for this modification? Thanks. Mike Heaven, PhD Principal Scientist p: (314) 628-1110 e: mik...@in...<mailto:mik...@in...> [cid:image002.png@01DB77C3.74F56950] LEGAL NOTICE This message is confidential and contains information which may be legally privileged. It is intended for the stated addressee(s) only. Access to this email by anyone else is unauthorized. If you are not the intended addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorized and is unlawful. If you are not the addressee, please inform the sender immediately and delete the original message. The data in this email will have been screened for the presence of computer viruses known by the Company at the time the email was produced. The Company cannot guarantee, however, that the email or any attachments are virus free. Delivery of the email will be at the addressee's risk. |
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From: Bielow, C. <Chr...@fu...> - 2024-08-19 13:53:27
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Dear all, the OpenMS team is pleased to announce the OpenMS User Meeting 2024 When: 17th - 18th October 2024 (Thursday - Friday) Where: Downtown Berlin, Germany What: · Basic introduction to data analysis with OpenMS (2 days, 17-18 Oct) led by Sam Wein. · Advanced Tutorial: pyOpenMS and web-apps (1 day, 17 Oct) led by Matteo Pilz and Axel Walter. · Advanced Tutorial: top-down proteomics with OpenMS (1 day, 17 Oct) led by Kyowon Jeong. · Advanced Tutorial: DIA proteomics with OpenSwath/OpenMS (1 day, 18 Oct) led by Joshua Charkow. Lunch, dinner, snacks, coffee, and tea will be provided. Afterwards, consider continuing your journey to <https://2024.hupo.org/> HUPO in nearby town of Dresden (separate event), or enjoy a weekend in Berlin. For more details, please visit the <https://openms.de/news/usermeeting2024/> OpenMS Homepage. We look forward to seeing you there! Best regards, The OpenMS Team -- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de |
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From: <hid...@id...> - 2024-05-30 05:23:31
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Hello there
This is the first time to post the question.
I have begun to use pyOpenMS recently.
(python 3.11.4, using VSCode)
How can I display mass spectrum (1Ddata) of a scan number which I select using pyOpenMS ?
I have found the code to display TIC of sample.
*******************************************
import numpy as np
import matplotlib.pyplot as plt
import pyopenms as oms
path = r"\test.mzML"
exp = oms.MSExperiment()
oms.MzMLFile().load(path,exp)
tic = exp.calculateTIC()
retention_times, intensities = tic.get_peaks()
plt.plot(retention_times, intensities)
plt.title('TIC')
plt.xlabel('time (s)')
plt.ylabel('intensity (cps)')
plt.show()
*******************************************
I can display TIC successfuly but I don't know how to display the mass spectrum of a scan number which I select.
Could anyone tell me which function of pyOpenMS to use (and sample code, if possible) ?
Regards
|
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From: mikky a. <osh...@gm...> - 2024-04-13 02:48:58
|
Hi, Thank you for the work you’ve all done with this platform. I am a beginner who is new to the platform so forgive my ignorance. I have some 13C labeled metabolomic data in conjunction with unlabelled data. Does the platform have a function to enable identification of enriched isotopes? If it does, please can you link me to the information. Thank you. Mikky |
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From: Shukur, M. R. M. <moh...@un...> - 2024-03-23 01:06:46
|
Dear OpenMS Team I am sending you this email regarding the material for the OpenMs-Knime. I am trying to download the package but send me error message: The server is temporarily unable to service your request due to maintenance downtime or capacity problems. Please try again later. ________________________________ Apache/2.4.41 (Ubuntu) Server at abibuilder.cs.uni-tuebingen.de Port 443 is there any other way to download the material package? Best Regards Mohanad ------------------------------------------------ Mohanad Shukur Faculty of Biology, Bio 27 Proteome and Metabolome Research Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany phone: +49 521 106 5627 email: moh...@un... |
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From: Simon R. <Sim...@un...> - 2024-02-07 10:16:48
|
Hallo Chris, es geht mir also um das 2. Problem. Mit dem nicht-lösen des 1. habe ich mich abgefunden. MfG Simon Redlich Am 07.02.2024 um 11:12 schrieb Simon Redlich: > > Hallo Chris, > > leider konnte ich keine zufriedenstellende Optionen für Openms finden > um das Mitteln der 100 Scans zu gewährleisten. Ich hoffe du kannst > dich an meinen Fall erinnern. > > Falls du dich erinnern kannst hatte ich davor ja ein anderes Problem, > für das wir eine Teams Unterhaltung hatten. Die einfache Lösung war > die raw-Datein einfach alle einzeln in das dta2d-Format umzuwandeln > und anschließend ein neues Programm zu schreiben welches diese ließt > uund in eine csv.-Datei umwandelt. In dem Moment meinte ich, dass das > eine valide Lösung wäre. Jedoch ist mir aufgefallen, dass ich > tatsächlich auf den "FeaturelinkerunlabeldQT" angewiesen bin. Wie in > der Abbildung unten zu sehen ist habe ich aber eine ziemlich > unaufgeräumte Pipeline, weil der obere "FeaturelinkerunlabeldQT" > meine Probenbezeichung zu "UNKNOWN" verändert. Daher benötige ich eine > zweite Pipeline die mir eine Datei erstellt, bei dem der Probenname > nicht umgewandelt wird. Das Prblem lag soweit ich mich erinnern kann > im featureXML welches in Nod 11 entsteht. Wäre es möglich sich dieses > Problem noch einmal widmen? > > > Ich hoffe Sie können sich erinnern. Falls nicht versuche ich das > Problem nocheinmal genauer zu beschreiben. > > Mit freundlichen Grüßen > > Simon Redlich > > Am 27.10.2023 um 12:58 schrieb sim...@un...: >> >> Hello Chris, >> >> I have a problem with the OpenMS 3.1.0-pre-nightly version. I tried >> to install the most of the available 3.1.0 versions from the website >> https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/ >> <https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/> >> >> Up till version 2023-10-13 I could not manage to install it because >> something was missing. From Version 2023-10-16 on I was able to >> install it but the following message was shown for 1 sec: >> >> This application failed to start because it could not find or load >> the Qt platform plugin “windows” in “”. Reinstall the application may >> fix this problem >> >> The same problem was showing for all newer version and reinstalling >> it was not the solution. I tried it on two different PCs with windows >> without success. >> >> To the remark to the last part “Ich hatte auch einen Screenshot in >> deinen GoogleDrive dateien gesehen fuer einen Labelfree Workflow von >> LC-MS Daten. Der waere aber fuer DirektInjection ungeeignet. >> >> Bin jetzt gerade nicht sicher warum dieser Workflow mit dabei war.“ >> >> I have the lablefree workflow in it because for some reason the >> workflow cant read the filename and gives me at the end a “UNKNOWN” >> for all samplenames in the Datasheet. The second Datasheet gives me >> the correct names. So I manually have to copy the sample names out of >> one datasheet into the one with my real data. Hope you understand. If >> not maybe we can talk in German. >> >> Maybe a additional problem that can be worked on as well to cancel >> out unnecessary nodes from the workflow. If necessary I can give you >> additional informations on the googledrive folder if this helps. >> >> Best regard Simon >> >> Hi Simon, >> >> I downloaded the data, looked at the problem and send you an email on >> Sept. 23rd. I copy it below (in german), for reference. >> >> Maybe it did not make it your inbox? >> >> Since I was at it now, I created a TOPPAS pipeline (attached) which >> 1) converts .Raw to mzmML 2) filters spectra based on RT range 3) >> merges whatever remains into a single MS1 spectrum. >> >> Some more annotation can be found in the workflow description when >> you open it in TOPPAS (see rightmost window named "Workflow >> Description" in TOPPAS). >> >> Hope this fits your needs. Feel free to get back in case something is >> unclear. >> >> cheers >> >> Chris >> >> ---- >> >> Dr. Chris Bielow >> >> Bioinformatics Solution Center (BSC) >> >> www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> >> >> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room >> K21, 14195 Berlin >> >> Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de >> >> ----- >> >> Hi Simon, >> >> Ich bin vor meinem Urlaub nicht mehr dazu gekommen dir zu antworten: >> >> Der SpectraMerger hatte einen Bug und konnte nicht mit deinen Daten >> funktionieren. Das ist mittlerweile gefixt und unter >> https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/ >> >> stehen tagesaktuelle Installationsdateien für verschiedene >> Betriebssysteme bereit. >> >> z.B. >> >> https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/OpenMS-3.1.0-pre-nightly-latest-Win64.exe >> >> fuer Windows 10/11. >> >> Das sollte dein Problem loesen. >> >> Ich hatte auch einen Screenshot in deinen GoogleDrive dateien gesehen >> fuer einen Labelfree Workflow von LC-MS Daten. Der waere aber fuer >> DirektInjection ungeeignet. >> >> Bin jetzt gerade nicht sicher warum dieser Workflow mit dabei war. >> >> Ich bin noch eine Woche im Urlaub, danach kann ich mir das gerne noch >> mal genauer anschauen, wenn es Bedarf gibt. >> >> Vg >> >> Chris >> >> -- >> >> Dr. Chris Bielow >> >> Bioinformatics Solution Center (BSC) >> >> www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> >> >> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room >> K21, 14195 Berlin >> >> Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de >> >> -----Original Message----- >> >> From: Simon Benjamin Redlich <sim...@un... >> <mailto:sim...@un...>> >> >> Sent: Thursday, October 19, 2023 11:04 AM >> >> To: General OpenMS discussion <ope...@li... >> <mailto:ope...@li...>> >> >> Subject: Re: [Open-ms-general] OpenMS Directinjection >> >> Hello Chris, >> >> are there any news about my request or did I overlooked a Email? I >> just noticed that Julianus Pfeuffer ask for permission for the >> googledrive folder. If there is no option to get the correct MS Data >> from the raw-Data without the xcalibur program, then we leave it like >> that. It just would be a dream to use just OpenMS for my pipeline. >> >> Best regard >> >> Simon Redlich >> >> Quoting sim...@un... <mailto:sim...@un...>: >> >> > Hi Chris, >> >> > sorry for the German. I can write it in English if you want. Steffen >> >> > sounded quite German so I thought it would be easier. Here the Link >> >> > https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2 >> <https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2> >> >> > Wk?usp=sharing >> >> > >> >> > Best Regards >> >> > Simon >> >> > >> >> > -----Original Message----- >> >> > From: Bielow, Chris <Chr...@fu... <mailto:Chr...@fu...>> >> >> > Sent: Freitag, 15. September 2023 14:35 >> >> > To: General OpenMS discussion <ope...@li... >> <mailto:ope...@li...>> >> >> > Subject: Re: [Open-ms-general] OpenMS Directinjection >> >> > >> >> > Hi Simon, >> >> > >> >> > the attachments did not arrive unfortunately. This may be due to the >> >> > way Sourceforge mailing lists are operated. >> >> > Can you upload the attachments, and ideally, the input mzML data that >> >> > you are trying to merge to some file upload service (e.g. >> >> > GoogleDrive, File.io, WeTransfer etc) and share the link here? >> >> > Alternatively you can open an issue on the OpenMS Github repository >> >> > and attach some files there. >> >> > Thanks! >> >> > >> >> > Cheers >> >> > Chris >> >> > >> >> > PS: could you solve your KNIME issue regarding MIME types? >> >> > >> >> > -- >> >> > Dr. Chris Bielow >> >> > >> >> > Bioinformatics Solution Center (BSC) >> >> > www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> >> >> > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room >> >> > K21, 14195 Berlin >> >> > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de >> >> > >> >> > -----Original Message----- >> >> > From: sim...@un... >> <mailto:sim...@un...><sim...@un... >> <mailto:sim...@un...>> >> >> > Sent: Friday, September 15, 2023 2:15 PM >> >> > To: 'Neumann, Steffen' <sne...@ip... <mailto:sne...@ip...>>; >> 'General OpenMS >> >> > discussion' <ope...@li... >> <mailto:ope...@li...>> >> >> > Subject: [Open-ms-general] OpenMS Directinjection >> >> > >> >> > Hallo Steffen, >> >> > aufgrund deines Namens hoffe ich, dass ich auf deutsch mit dir >> >> > schreiben kann. Vielen Dank für deine Hilfe. >> >> > Mein nächstes Anliegen an dich ist eher ein Longshot, da ich nicht >> >> > weiß, wie gut du dich mit HR-MS auskennen. Ich versuche zur Zeit >> >> > mithilfe von OpenMS Direct Injectionen in tsv-Dateien umzuwandeln. >> >> > Mein Work-flow ist im ersten Bild zu sehen. Mein Ziel ist es die >> >> > centroid Daten (also Signale) unterschiedlichen Messungen in eine tsv >> >> > Datei zu kombieren. Bevor das aber passieren kann, muss ich zur Zeit >> >> > händisch jede Messung aufrufen und dort den gewünschten >> >> > Retentionszeibereich markieren um ein Massenspektrum mehrerer Scans zu >> >> > erhalten. Dieses Massenspektrum muss dann erneut als raw-Datei >> >> > exportiert werden. Dazu benötige ich Xcalibur (QualBrowser) von >> >> > ThermoFisher (wie sie in Bild 2 zu sehen ist). Die neu erstellten >> >> > raw-Dateien kann dann OpenMS ohne Probleme lesen, zur mzML-Datei >> >> > umwandeln und in einer tsv-Datei kombinieren. Die Bilder sind in der >> >> > Powerpoint enthalten >> >> > >> >> > Ich würde gerne OpenMS dazu nutzen mir diesen manuellen Teil >> >> > abzunehmen. Ich denke, dass der SpectraMerger mithilfe der >> >> > Block_method da weiterhelfen könnte. Leider kommt jedesmal der Fehler: >> >> > " Error: Unexpected internal error (the given size was not >> >> > expected: 0)". Leider schaffe ich es nicht diesen Fehler zu beheben. >> >> > Außerdem wird mir die Fehlermeldung: >> >> > " TOPPBase.cpp(1634): Error occurred in line 134 of file >> >> > E:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\t >> >> > opp\SpectraMerger.cpp (in function: enum OpenMS::TOPPBase::ExitCodes >> __cdecl TOPPSpectraMerger::main_(int,const char **)) !" ausgegeben >> wenn ich Debug aktiviere. Vielleicht hilft es ja. >> >> > >> >> > Ich kenne mich leider nur geringfügig mit Informatik aus und kann >> >> > damit wenig anfangen. >> >> > Falls du eine Möglichkeit kennst das zu beheben oder eine andere >> >> > Möglichkeit kennst mein Ziel mit openMS zu erreichen, auch gerne mit >> >> > anderen Nodes, dann würde ich mich sehr freuen und wäre dir sehr >> >> > dankbar, da dadurch mein Workflow deutlich schlanker werden würde. >> >> > Dadurch wird meine geplante Publikation übersichtlicher und wäre zu >> >> > 100% open source. >> >> > Ich hoffe du verstehst meine Probleme und mein Anliegen. >> >> > Falls du mir nicht weiterhelfen kannst, möchte ich trotzdem bei dir >> >> > für die investierte Zeit bedanken. >> >> > >> >> > Mit freundlichen Grüßen >> >> > Simon Redlich >> >> > >> >> > >> >> > -----Original Message----- >> >> > From: Neumann, Steffen <sne...@ip... <mailto:sne...@ip...>> >> >> > Sent: Donnerstag, 7. September 2023 17:25 >> >> > To: ope...@li... >> <mailto:ope...@li...> >> >> > Subject: Re: [Open-ms-general] Question to Internal Calibration >> >> > >> >> > Hi, >> >> > >> >> > side-comment: if the path to rscript.exe includes the R version, >> >> > you'll likely have to change that in case you update R and remove the >> >> > old version of R, or the Knome node will stop working. Unless you want >> >> > to install multiple versions of R, you could install it into a path >> >> > without version. >> >> > >> >> > As I don't know Windows and not too much Knime, I can't help with the >> >> > other problem. >> >> > >> >> > Another side comment: instead of the customer support, you are >> >> > reaching here the developers, power users and generally helpful OpenMS >> >> > community >> >> > :-) >> >> > >> >> > Grüsse nach Jena, >> >> > Yours, >> >> > Steffen >> >> > >> >> > >> >> > >> >> > >> >> > On Thu, 2023-09-07 at 13:24 +0200, sim...@un... >> <mailto:sim...@un...>wrote: >> >> >> Hello Chris, >> >> >> thank for your fast respond. >> >> >> I found the rscript.exe but if I check the File Extension (override)- >> >> >> box and keep it empty like in your picture KNIME starts to show the >> >> >> problem “invalid settings: no file extension (override) provided. No >> >> >> matter what I type in the box as alternative extension its not what >> >> >> the node wants to have. So, in summary: I could figure out some of my >> >> >> problems but I’m still stuck and can’t run the node. >> >> >> >> >> >> Best regards Simon >> >> >> >> >> >> From: Bielow, Chris <Chr...@fu... >> <mailto:Chr...@fu...>> >> >> >> Sent: Mittwoch, 6. September 2023 12:18 >> >> >> To: General OpenMS discussion <ope...@li... >> <mailto:ope...@li...>> >> >> >> Subject: Re: [Open-ms-general] Question to Internal Calibration >> >> >> >> >> >> Hi Simon, >> >> >> >> >> >> the build-in default value of ‚Rscript‘ does not work in your case >> >> >> because in general KNIME does not provide the PATH environment to the >> >> >> nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration >> >> >> cannot find the ‘Rscript’ executable and you must point to it >> >> >> manually. >> >> >> Depending on the system you are on, the location of the ‘Rscript’ >> >> >> executable will differ. >> >> >> One easy way to find it, is to use the build-in search functionality >> >> >> of your operating system, i.e. the Windows Explorer, Nautilus, Finder >> >> >> etc. >> >> >> If you are familiar with the commandline, try “where rscript” (for >> >> >> Windows) or “which Rscript” (for Linux/Mac). This should give you the >> >> >> desired path, if the R programming language was properly installed on >> >> >> your system. >> >> >> If you run KNIME on Windows, you need to check the ‘File Extension >> >> >> (override)` box, otherwise KNIME will complain that Rscript has an >> >> >> ‘.exe’ extension – see attached image. >> >> >> >> >> >> Hope this helps. >> >> >> >> >> >> Cheers >> >> >> Chris >> >> >> >> >> >> >> >> >> -- >> >> >> Dr. Chris Bielow >> >> >> >> >> >> Bioinformatics Solution Center (BSC) >> >> >> www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> >> >> >> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room >> >> >> K21, 14195 Berlin >> >> >> Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de >> >> >> >> >> >> From: sim...@un... >> <mailto:sim...@un...><sim...@un... >> <mailto:sim...@un...>> >> >> >> Sent: Tuesday, September 5, 2023 1:16 PM >> >> >> To: ope...@li... >> <mailto:ope...@li...> >> >> >> Subject: [Open-ms-general] Question to Internal Calibration >> >> >> >> >> >> Dear customer service, >> >> >> I have a question regarding the internal calibration node. I >> >> >> personally prefer to work with OpenMS in the Knime platform. Now I >> >> >> stumbled over a problem with the internal calibration node in the >> >> >> Knimesoftware. The node in the OpenMS toppas is working fine because >> >> >> there the “rscript execution” is already embedded. For the node in >> >> >> the Knime platform this embedded “rscript execution” is missing and I >> >> >> must add an input file node with connection to the the calibration >> >> >> node. I cant find the rscript that is mentioned. >> >> >> >> >> >> I hope I write to the correct person to tackle that problem. If note >> >> >> maybe you can direct me to the right address or forum. >> >> >> Thanks in advance for your time and hopefully a answers to my >> >> >> question. >> >> >> >> >> >> Best Regards >> >> >> Simon Redlich >> >> >> _______________________________________________ >> >> >> Open-ms-general mailing list >> >> >> Ope...@li... >> <mailto:Ope...@li...> >> >> >> https://lists.sourceforge.net/lists/listinfo/open-ms-general >> <https://lists.sourceforge.net/lists/listinfo/open-ms-general> >> >> > >> >> > -- >> >> > IPB is hiring: >> >> > * Researcher (PostDoc Cheminformatics) (m/f/d) >> >> > https://www.ipb-halle.de/en/career/job-vacancies/joboffer- >> >> > detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd >> >> > / >> >> > >> >> > Upcoming events: >> >> > * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe >> >> > https://www.nfdi.de/cordi-2023/?lang=en >> <https://www.nfdi.de/cordi-2023/?lang=en> >> >> > >> >> > * DGMet September 27th to 29th, 2023, Halle (Saale) >> >> > https://dgmet.de/event/dgmet-annual-meeting/ >> <https://dgmet.de/event/dgmet-annual-meeting/> >> >> > >> >> > * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld >> >> > https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 >> >> > >> >> > >> >> > --- >> >> > IPB Halle Computational Plant Biochemistry (CPB) >> >> > Dr. Steffen Neumann http://www.IPB-Halle.DE <http://www.IPB-Halle.DE> >> >> > Weinberg 3 Tel. +49 (0) 345 5582 - 1470 >> >> > 06120 Halle +49 (0) 345 5582 - 0 >> >> > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Open-ms-general mailing list >> >> > Ope...@li... >> <mailto:Ope...@li...> >> >> > https://lists.sourceforge.net/lists/listinfo/open-ms-general >> <https://lists.sourceforge.net/lists/listinfo/open-ms-general> >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Open-ms-general mailing list >> >> > Ope...@li... >> <mailto:Ope...@li...> >> >> > https://lists.sourceforge.net/lists/listinfo/open-ms-general >> <https://lists.sourceforge.net/lists/listinfo/open-ms-general> >> >> > >> >> > >> >> > >> >> > _______________________________________________ >> >> > Open-ms-general mailing list >> >> > Ope...@li... >> <mailto:Ope...@li...> >> >> > https://lists.sourceforge.net/lists/listinfo/open-ms-general >> <https://lists.sourceforge.net/lists/listinfo/open-ms-general> >> >> -- >> >> Simon Redlich, >> >> Friedrich-Schiller-Universität Jena >> >> Institut for Anorganic and Analytical Chemistry Lessingstr. 8 >> >> 07743 Jena >> >> Germany >> >> +493641(9)48288 >> >> _______________________________________________ >> >> Open-ms-general mailing list >> >> Ope...@li... >> <mailto:Ope...@li...> >> >> https://lists.sourceforge.net/lists/listinfo/open-ms-general >> <https://lists.sourceforge.net/lists/listinfo/open-ms-general> >> >> >> >> _______________________________________________ >> Open-ms-general mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/open-ms-general > > > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general |
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From: Simon R. <Sim...@un...> - 2024-02-07 10:12:19
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Hallo Chris, leider konnte ich keine zufriedenstellende Optionen für Openms finden um das Mitteln der 100 Scans zu gewährleisten. Ich hoffe du kannst dich an meinen Fall erinnern. Falls du dich erinnern kannst hatte ich davor ja ein anderes Problem, für das wir eine Teams Unterhaltung hatten. Die einfache Lösung war die raw-Datein einfach alle einzeln in das dta2d-Format umzuwandeln und anschließend ein neues Programm zu schreiben welches diese ließt uund in eine csv.-Datei umwandelt. In dem Moment meinte ich, dass das eine valide Lösung wäre. Jedoch ist mir aufgefallen, dass ich tatsächlich auf den "FeaturelinkerunlabeldQT" angewiesen bin. Wie in der Abbildung unten zu sehen ist habe ich aber eine ziemlich unaufgeräumte Pipeline, weil der obere "FeaturelinkerunlabeldQT" meine Probenbezeichung zu "UNKNOWN" verändert. Daher benötige ich eine zweite Pipeline die mir eine Datei erstellt, bei dem der Probenname nicht umgewandelt wird. Das Prblem lag soweit ich mich erinnern kann im featureXML welches in Nod 11 entsteht. Wäre es möglich sich dieses Problem noch einmal widmen? Ich hoffe Sie können sich erinnern. Falls nicht versuche ich das Problem nocheinmal genauer zu beschreiben. Mit freundlichen Grüßen Simon Redlich Am 27.10.2023 um 12:58 schrieb sim...@un...: > > Hello Chris, > > I have a problem with the OpenMS 3.1.0-pre-nightly version. I tried to > install the most of the available 3.1.0 versions from the website > https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/ > <https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/> > > Up till version 2023-10-13 I could not manage to install it because > something was missing. From Version 2023-10-16 on I was able to > install it but the following message was shown for 1 sec: > > This application failed to start because it could not find or load the > Qt platform plugin “windows” in “”. Reinstall the application may fix > this problem > > The same problem was showing for all newer version and reinstalling it > was not the solution. I tried it on two different PCs with windows > without success. > > To the remark to the last part “Ich hatte auch einen Screenshot in > deinen GoogleDrive dateien gesehen fuer einen Labelfree Workflow von > LC-MS Daten. Der waere aber fuer DirektInjection ungeeignet. > > Bin jetzt gerade nicht sicher warum dieser Workflow mit dabei war.“ > > I have the lablefree workflow in it because for some reason the > workflow cant read the filename and gives me at the end a “UNKNOWN” > for all samplenames in the Datasheet. The second Datasheet gives me > the correct names. So I manually have to copy the sample names out of > one datasheet into the one with my real data. Hope you understand. If > not maybe we can talk in German. > > Maybe a additional problem that can be worked on as well to cancel out > unnecessary nodes from the workflow. If necessary I can give you > additional informations on the googledrive folder if this helps. > > Best regard Simon > > Hi Simon, > > I downloaded the data, looked at the problem and send you an email on > Sept. 23rd. I copy it below (in german), for reference. > > Maybe it did not make it your inbox? > > Since I was at it now, I created a TOPPAS pipeline (attached) which 1) > converts .Raw to mzmML 2) filters spectra based on RT range 3) merges > whatever remains into a single MS1 spectrum. > > Some more annotation can be found in the workflow description when you > open it in TOPPAS (see rightmost window named "Workflow Description" > in TOPPAS). > > Hope this fits your needs. Feel free to get back in case something is > unclear. > > cheers > > Chris > > ---- > > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > > www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> > > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > ----- > > Hi Simon, > > Ich bin vor meinem Urlaub nicht mehr dazu gekommen dir zu antworten: > > Der SpectraMerger hatte einen Bug und konnte nicht mit deinen Daten > funktionieren. Das ist mittlerweile gefixt und unter > https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/ > > stehen tagesaktuelle Installationsdateien für verschiedene > Betriebssysteme bereit. > > z.B. > > https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/OpenMS-3.1.0-pre-nightly-latest-Win64.exe > > fuer Windows 10/11. > > Das sollte dein Problem loesen. > > Ich hatte auch einen Screenshot in deinen GoogleDrive dateien gesehen > fuer einen Labelfree Workflow von LC-MS Daten. Der waere aber fuer > DirektInjection ungeeignet. > > Bin jetzt gerade nicht sicher warum dieser Workflow mit dabei war. > > Ich bin noch eine Woche im Urlaub, danach kann ich mir das gerne noch > mal genauer anschauen, wenn es Bedarf gibt. > > Vg > > Chris > > -- > > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > > www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> > > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > -----Original Message----- > > From: Simon Benjamin Redlich <sim...@un... > <mailto:sim...@un...>> > > Sent: Thursday, October 19, 2023 11:04 AM > > To: General OpenMS discussion <ope...@li... > <mailto:ope...@li...>> > > Subject: Re: [Open-ms-general] OpenMS Directinjection > > Hello Chris, > > are there any news about my request or did I overlooked a Email? I > just noticed that Julianus Pfeuffer ask for permission for the > googledrive folder. If there is no option to get the correct MS Data > from the raw-Data without the xcalibur program, then we leave it like > that. It just would be a dream to use just OpenMS for my pipeline. > > Best regard > > Simon Redlich > > Quoting sim...@un... <mailto:sim...@un...>: > > > Hi Chris, > > > sorry for the German. I can write it in English if you want. Steffen > > > sounded quite German so I thought it would be easier. Here the Link > > > https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2 > <https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2> > > > Wk?usp=sharing > > > > > > Best Regards > > > Simon > > > > > > -----Original Message----- > > > From: Bielow, Chris <Chr...@fu... <mailto:Chr...@fu...>> > > > Sent: Freitag, 15. September 2023 14:35 > > > To: General OpenMS discussion <ope...@li... > <mailto:ope...@li...>> > > > Subject: Re: [Open-ms-general] OpenMS Directinjection > > > > > > Hi Simon, > > > > > > the attachments did not arrive unfortunately. This may be due to the > > > way Sourceforge mailing lists are operated. > > > Can you upload the attachments, and ideally, the input mzML data that > > > you are trying to merge to some file upload service (e.g. > > > GoogleDrive, File.io, WeTransfer etc) and share the link here? > > > Alternatively you can open an issue on the OpenMS Github repository > > > and attach some files there. > > > Thanks! > > > > > > Cheers > > > Chris > > > > > > PS: could you solve your KNIME issue regarding MIME types? > > > > > > -- > > > Dr. Chris Bielow > > > > > > Bioinformatics Solution Center (BSC) > > > www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> > > > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > > > K21, 14195 Berlin > > > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > > > > > -----Original Message----- > > > From: sim...@un... > <mailto:sim...@un...><sim...@un... > <mailto:sim...@un...>> > > > Sent: Friday, September 15, 2023 2:15 PM > > > To: 'Neumann, Steffen' <sne...@ip... <mailto:sne...@ip...>>; > 'General OpenMS > > > discussion' <ope...@li... > <mailto:ope...@li...>> > > > Subject: [Open-ms-general] OpenMS Directinjection > > > > > > Hallo Steffen, > > > aufgrund deines Namens hoffe ich, dass ich auf deutsch mit dir > > > schreiben kann. Vielen Dank für deine Hilfe. > > > Mein nächstes Anliegen an dich ist eher ein Longshot, da ich nicht > > > weiß, wie gut du dich mit HR-MS auskennen. Ich versuche zur Zeit > > > mithilfe von OpenMS Direct Injectionen in tsv-Dateien umzuwandeln. > > > Mein Work-flow ist im ersten Bild zu sehen. Mein Ziel ist es die > > > centroid Daten (also Signale) unterschiedlichen Messungen in eine tsv > > > Datei zu kombieren. Bevor das aber passieren kann, muss ich zur Zeit > > > händisch jede Messung aufrufen und dort den gewünschten > > > Retentionszeibereich markieren um ein Massenspektrum mehrerer Scans zu > > > erhalten. Dieses Massenspektrum muss dann erneut als raw-Datei > > > exportiert werden. Dazu benötige ich Xcalibur (QualBrowser) von > > > ThermoFisher (wie sie in Bild 2 zu sehen ist). Die neu erstellten > > > raw-Dateien kann dann OpenMS ohne Probleme lesen, zur mzML-Datei > > > umwandeln und in einer tsv-Datei kombinieren. Die Bilder sind in der > > > Powerpoint enthalten > > > > > > Ich würde gerne OpenMS dazu nutzen mir diesen manuellen Teil > > > abzunehmen. Ich denke, dass der SpectraMerger mithilfe der > > > Block_method da weiterhelfen könnte. Leider kommt jedesmal der Fehler: > > > " Error: Unexpected internal error (the given size was not > > > expected: 0)". Leider schaffe ich es nicht diesen Fehler zu beheben. > > > Außerdem wird mir die Fehlermeldung: > > > " TOPPBase.cpp(1634): Error occurred in line 134 of file > > > E:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\t > > > opp\SpectraMerger.cpp (in function: enum OpenMS::TOPPBase::ExitCodes > __cdecl TOPPSpectraMerger::main_(int,const char **)) !" ausgegeben > wenn ich Debug aktiviere. Vielleicht hilft es ja. > > > > > > Ich kenne mich leider nur geringfügig mit Informatik aus und kann > > > damit wenig anfangen. > > > Falls du eine Möglichkeit kennst das zu beheben oder eine andere > > > Möglichkeit kennst mein Ziel mit openMS zu erreichen, auch gerne mit > > > anderen Nodes, dann würde ich mich sehr freuen und wäre dir sehr > > > dankbar, da dadurch mein Workflow deutlich schlanker werden würde. > > > Dadurch wird meine geplante Publikation übersichtlicher und wäre zu > > > 100% open source. > > > Ich hoffe du verstehst meine Probleme und mein Anliegen. > > > Falls du mir nicht weiterhelfen kannst, möchte ich trotzdem bei dir > > > für die investierte Zeit bedanken. > > > > > > Mit freundlichen Grüßen > > > Simon Redlich > > > > > > > > > -----Original Message----- > > > From: Neumann, Steffen <sne...@ip... <mailto:sne...@ip...>> > > > Sent: Donnerstag, 7. September 2023 17:25 > > > To: ope...@li... > <mailto:ope...@li...> > > > Subject: Re: [Open-ms-general] Question to Internal Calibration > > > > > > Hi, > > > > > > side-comment: if the path to rscript.exe includes the R version, > > > you'll likely have to change that in case you update R and remove the > > > old version of R, or the Knome node will stop working. Unless you want > > > to install multiple versions of R, you could install it into a path > > > without version. > > > > > > As I don't know Windows and not too much Knime, I can't help with the > > > other problem. > > > > > > Another side comment: instead of the customer support, you are > > > reaching here the developers, power users and generally helpful OpenMS > > > community > > > :-) > > > > > > Grüsse nach Jena, > > > Yours, > > > Steffen > > > > > > > > > > > > > > > On Thu, 2023-09-07 at 13:24 +0200, sim...@un... > <mailto:sim...@un...>wrote: > > >> Hello Chris, > > >> thank for your fast respond. > > >> I found the rscript.exe but if I check the File Extension (override)- > > >> box and keep it empty like in your picture KNIME starts to show the > > >> problem “invalid settings: no file extension (override) provided. No > > >> matter what I type in the box as alternative extension its not what > > >> the node wants to have. So, in summary: I could figure out some of my > > >> problems but I’m still stuck and can’t run the node. > > >> > > >> Best regards Simon > > >> > > >> From: Bielow, Chris <Chr...@fu... > <mailto:Chr...@fu...>> > > >> Sent: Mittwoch, 6. September 2023 12:18 > > >> To: General OpenMS discussion <ope...@li... > <mailto:ope...@li...>> > > >> Subject: Re: [Open-ms-general] Question to Internal Calibration > > >> > > >> Hi Simon, > > >> > > >> the build-in default value of ‚Rscript‘ does not work in your case > > >> because in general KNIME does not provide the PATH environment to the > > >> nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration > > >> cannot find the ‘Rscript’ executable and you must point to it > > >> manually. > > >> Depending on the system you are on, the location of the ‘Rscript’ > > >> executable will differ. > > >> One easy way to find it, is to use the build-in search functionality > > >> of your operating system, i.e. the Windows Explorer, Nautilus, Finder > > >> etc. > > >> If you are familiar with the commandline, try “where rscript” (for > > >> Windows) or “which Rscript” (for Linux/Mac). This should give you the > > >> desired path, if the R programming language was properly installed on > > >> your system. > > >> If you run KNIME on Windows, you need to check the ‘File Extension > > >> (override)` box, otherwise KNIME will complain that Rscript has an > > >> ‘.exe’ extension – see attached image. > > >> > > >> Hope this helps. > > >> > > >> Cheers > > >> Chris > > >> > > >> > > >> -- > > >> Dr. Chris Bielow > > >> > > >> Bioinformatics Solution Center (BSC) > > >> www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> > > >> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > > >> K21, 14195 Berlin > > >> Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > >> > > >> From: sim...@un... > <mailto:sim...@un...><sim...@un... > <mailto:sim...@un...>> > > >> Sent: Tuesday, September 5, 2023 1:16 PM > > >> To: ope...@li... > <mailto:ope...@li...> > > >> Subject: [Open-ms-general] Question to Internal Calibration > > >> > > >> Dear customer service, > > >> I have a question regarding the internal calibration node. I > > >> personally prefer to work with OpenMS in the Knime platform. Now I > > >> stumbled over a problem with the internal calibration node in the > > >> Knimesoftware. The node in the OpenMS toppas is working fine because > > >> there the “rscript execution” is already embedded. For the node in > > >> the Knime platform this embedded “rscript execution” is missing and I > > >> must add an input file node with connection to the the calibration > > >> node. I cant find the rscript that is mentioned. > > >> > > >> I hope I write to the correct person to tackle that problem. If note > > >> maybe you can direct me to the right address or forum. > > >> Thanks in advance for your time and hopefully a answers to my > > >> question. > > >> > > >> Best Regards > > >> Simon Redlich > > >> _______________________________________________ > > >> Open-ms-general mailing list > > >> Ope...@li... > <mailto:Ope...@li...> > > >> https://lists.sourceforge.net/lists/listinfo/open-ms-general > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> > > > > > > -- > > > IPB is hiring: > > > * Researcher (PostDoc Cheminformatics) (m/f/d) > > > https://www.ipb-halle.de/en/career/job-vacancies/joboffer- > > > detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd > > > / > > > > > > Upcoming events: > > > * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe > > > https://www.nfdi.de/cordi-2023/?lang=en > <https://www.nfdi.de/cordi-2023/?lang=en> > > > > > > * DGMet September 27th to 29th, 2023, Halle (Saale) > > > https://dgmet.de/event/dgmet-annual-meeting/ > <https://dgmet.de/event/dgmet-annual-meeting/> > > > > > > * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld > > > https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 > > > > > > > > > --- > > > IPB Halle Computational Plant Biochemistry (CPB) > > > Dr. Steffen Neumann http://www.IPB-Halle.DE <http://www.IPB-Halle.DE> > > > Weinberg 3 Tel. +49 (0) 345 5582 - 1470 > > > 06120 Halle +49 (0) 345 5582 - 0 > > > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Open-ms-general mailing list > > > Ope...@li... > <mailto:Ope...@li...> > > > https://lists.sourceforge.net/lists/listinfo/open-ms-general > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> > > > > > > > > > > > > _______________________________________________ > > > Open-ms-general mailing list > > > Ope...@li... > <mailto:Ope...@li...> > > > https://lists.sourceforge.net/lists/listinfo/open-ms-general > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> > > > > > > > > > > > > _______________________________________________ > > > Open-ms-general mailing list > > > Ope...@li... > <mailto:Ope...@li...> > > > https://lists.sourceforge.net/lists/listinfo/open-ms-general > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> > > -- > > Simon Redlich, > > Friedrich-Schiller-Universität Jena > > Institut for Anorganic and Analytical Chemistry Lessingstr. 8 > > 07743 Jena > > Germany > > +493641(9)48288 > > _______________________________________________ > > Open-ms-general mailing list > > Ope...@li... > <mailto:Ope...@li...> > > https://lists.sourceforge.net/lists/listinfo/open-ms-general > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> > > > > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general |
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From: damian i. <dam...@gm...> - 2023-12-18 16:29:04
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Dear colleagues, We are currently in the process of validating specific peptides de novo from data obtained in Orbitrap. We have used the DenovoGui program for this de novo analysis. At this moment, we are working on determining the validity of the obtained sequences. To achieve this, we attempted to use ToppView; however, we encountered some issues, such as all peaks in the theoretical spectrum having an intensity of 100%, and we couldn't find a Pearson or similar value that could validate our peptides. Therefore, we would like to inquire about any suggestions you could provide to help us resolve these issues. Alternatively, you may recommend another freely accessible graphical environment program. Best regards, Lic. Damián Ibarra Laboratorio de Biología Ósea Universidad Nacional de Rosario Santa Fe 3100 - (2000) - Rosario - Santa Fe - Argentina Tel: (+54) 341 4362300 <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> Libre de virus.www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> |
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From: Bielow, C. <Chr...@fu...> - 2023-11-01 10:51:05
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Hi Simon, your workflows are rather specific, so lets take the discussion offline. Concerning the Windows installer: I will have a closer look, once I get my hands on a fresh Windows10. Cheers Chris -- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de From: sim...@un... <sim...@un...> Sent: Friday, October 27, 2023 12:58 PM To: ope...@li... Subject: [Open-ms-general] OpenMS 3.1.0-pre-nightly does not work Hello Chris, I have a problem with the OpenMS 3.1.0-pre-nightly version. I tried to install the most of the available 3.1.0 versions from the website <https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/night ly/> https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightl y/ Up till version 2023-10-13 I could not manage to install it because something was missing. From Version 2023-10-16 on I was able to install it but the following message was shown for 1 sec: This application failed to start because it could not find or load the Qt platform plugin windows in . Reinstall the application may fix this problem The same problem was showing for all newer version and reinstalling it was not the solution. I tried it on two different PCs with windows without success. To the remark to the last part Ich hatte auch einen Screenshot in deinen GoogleDrive dateien gesehen fuer einen Labelfree Workflow von LC-MS Daten. Der waere aber fuer DirektInjection ungeeignet. Bin jetzt gerade nicht sicher warum dieser Workflow mit dabei war. I have the lablefree workflow in it because for some reason the workflow cant read the filename and gives me at the end a UNKNOWN for all samplenames in the Datasheet. The second Datasheet gives me the correct names. So I manually have to copy the sample names out of one datasheet into the one with my real data. Hope you understand. If not maybe we can talk in German. Maybe a additional problem that can be worked on as well to cancel out unnecessary nodes from the workflow. If necessary I can give you additional informations on the googledrive folder if this helps. Best regard Simon Hi Simon, I downloaded the data, looked at the problem and send you an email on Sept. 23rd. I copy it below (in german), for reference. Maybe it did not make it your inbox? Since I was at it now, I created a TOPPAS pipeline (attached) which 1) converts .Raw to mzmML 2) filters spectra based on RT range 3) merges whatever remains into a single MS1 spectrum. Some more annotation can be found in the workflow description when you open it in TOPPAS (see rightmost window named "Workflow Description" in TOPPAS). Hope this fits your needs. Feel free to get back in case something is unclear. cheers Chris ---- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de ----- Hi Simon, Ich bin vor meinem Urlaub nicht mehr dazu gekommen dir zu antworten: Der SpectraMerger hatte einen Bug und konnte nicht mit deinen Daten funktionieren. Das ist mittlerweile gefixt und unter https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightl y/ stehen tagesaktuelle Installationsdateien für verschiedene Betriebssysteme bereit. z.B. https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightl y/OpenMS-3.1.0-pre-nightly-latest-Win64.exe fuer Windows 10/11. Das sollte dein Problem loesen. Ich hatte auch einen Screenshot in deinen GoogleDrive dateien gesehen fuer einen Labelfree Workflow von LC-MS Daten. Der waere aber fuer DirektInjection ungeeignet. Bin jetzt gerade nicht sicher warum dieser Workflow mit dabei war. Ich bin noch eine Woche im Urlaub, danach kann ich mir das gerne noch mal genauer anschauen, wenn es Bedarf gibt. Vg Chris -- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de -----Original Message----- From: Simon Benjamin Redlich < <mailto:sim...@un...> sim...@un...> Sent: Thursday, October 19, 2023 11:04 AM To: General OpenMS discussion < <mailto:ope...@li...> ope...@li...> Subject: Re: [Open-ms-general] OpenMS Directinjection Hello Chris, are there any news about my request or did I overlooked a Email? I just noticed that Julianus Pfeuffer ask for permission for the googledrive folder. If there is no option to get the correct MS Data from the raw-Data without the xcalibur program, then we leave it like that. It just would be a dream to use just OpenMS for my pipeline. Best regard Simon Redlich Quoting <mailto:sim...@un...> sim...@un...: > Hi Chris, > sorry for the German. I can write it in English if you want. Steffen > sounded quite German so I thought it would be easier. Here the Link > <https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2> https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2 > Wk?usp=sharing > > Best Regards > Simon > > -----Original Message----- > From: Bielow, Chris < <mailto:Chr...@fu...> Chr...@fu...> > Sent: Freitag, 15. September 2023 14:35 > To: General OpenMS discussion < <mailto:ope...@li...> ope...@li...> > Subject: Re: [Open-ms-general] OpenMS Directinjection > > Hi Simon, > > the attachments did not arrive unfortunately. This may be due to the > way Sourceforge mailing lists are operated. > Can you upload the attachments, and ideally, the input mzML data that > you are trying to merge to some file upload service (e.g. > GoogleDrive, File.io, WeTransfer etc) and share the link here? > Alternatively you can open an issue on the OpenMS Github repository > and attach some files there. > Thanks! > > Cheers > Chris > > PS: could you solve your KNIME issue regarding MIME types? > > -- > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > -----Original Message----- > From: <mailto:sim...@un...> sim...@un... < <mailto:sim...@un...> sim...@un...> > Sent: Friday, September 15, 2023 2:15 PM > To: 'Neumann, Steffen' < <mailto:sne...@ip...> sne...@ip...>; 'General OpenMS > discussion' < <mailto:ope...@li...> ope...@li...> > Subject: [Open-ms-general] OpenMS Directinjection > > Hallo Steffen, > aufgrund deines Namens hoffe ich, dass ich auf deutsch mit dir > schreiben kann. Vielen Dank für deine Hilfe. > Mein nächstes Anliegen an dich ist eher ein Longshot, da ich nicht > weiß, wie gut du dich mit HR-MS auskennen. Ich versuche zur Zeit > mithilfe von OpenMS Direct Injectionen in tsv-Dateien umzuwandeln. > Mein Work-flow ist im ersten Bild zu sehen. Mein Ziel ist es die > centroid Daten (also Signale) unterschiedlichen Messungen in eine tsv > Datei zu kombieren. Bevor das aber passieren kann, muss ich zur Zeit > händisch jede Messung aufrufen und dort den gewünschten > Retentionszeibereich markieren um ein Massenspektrum mehrerer Scans zu > erhalten. Dieses Massenspektrum muss dann erneut als raw-Datei > exportiert werden. Dazu benötige ich Xcalibur (QualBrowser) von > ThermoFisher (wie sie in Bild 2 zu sehen ist). Die neu erstellten > raw-Dateien kann dann OpenMS ohne Probleme lesen, zur mzML-Datei > umwandeln und in einer tsv-Datei kombinieren. Die Bilder sind in der > Powerpoint enthalten > > Ich würde gerne OpenMS dazu nutzen mir diesen manuellen Teil > abzunehmen. Ich denke, dass der SpectraMerger mithilfe der > Block_method da weiterhelfen könnte. Leider kommt jedesmal der Fehler: > " Error: Unexpected internal error (the given size was not > expected: 0)". Leider schaffe ich es nicht diesen Fehler zu beheben. > Außerdem wird mir die Fehlermeldung: > " TOPPBase.cpp(1634): Error occurred in line 134 of file > E:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\t > opp\SpectraMerger.cpp (in function: enum OpenMS::TOPPBase::ExitCodes __cdecl TOPPSpectraMerger::main_(int,const char **)) !" ausgegeben wenn ich Debug aktiviere. Vielleicht hilft es ja. > > Ich kenne mich leider nur geringfügig mit Informatik aus und kann > damit wenig anfangen. > Falls du eine Möglichkeit kennst das zu beheben oder eine andere > Möglichkeit kennst mein Ziel mit openMS zu erreichen, auch gerne mit > anderen Nodes, dann würde ich mich sehr freuen und wäre dir sehr > dankbar, da dadurch mein Workflow deutlich schlanker werden würde. > Dadurch wird meine geplante Publikation übersichtlicher und wäre zu > 100% open source. > Ich hoffe du verstehst meine Probleme und mein Anliegen. > Falls du mir nicht weiterhelfen kannst, möchte ich trotzdem bei dir > für die investierte Zeit bedanken. > > Mit freundlichen Grüßen > Simon Redlich > > > -----Original Message----- > From: Neumann, Steffen < <mailto:sne...@ip...> sne...@ip...> > Sent: Donnerstag, 7. September 2023 17:25 > To: <mailto:ope...@li...> ope...@li... > Subject: Re: [Open-ms-general] Question to Internal Calibration > > Hi, > > side-comment: if the path to rscript.exe includes the R version, > you'll likely have to change that in case you update R and remove the > old version of R, or the Knome node will stop working. Unless you want > to install multiple versions of R, you could install it into a path > without version. > > As I don't know Windows and not too much Knime, I can't help with the > other problem. > > Another side comment: instead of the customer support, you are > reaching here the developers, power users and generally helpful OpenMS > community > :-) > > Grüsse nach Jena, > Yours, > Steffen > > > > > On Thu, 2023-09-07 at 13:24 +0200, <mailto:sim...@un...> sim...@un... wrote: >> Hello Chris, >> thank for your fast respond. >> I found the rscript.exe but if I check the File Extension (override)- >> box and keep it empty like in your picture KNIME starts to show the >> problem invalid settings: no file extension (override) provided. No >> matter what I type in the box as alternative extension its not what >> the node wants to have. So, in summary: I could figure out some of my >> problems but Im still stuck and cant run the node. >> >> Best regards Simon >> >> From: Bielow, Chris < <mailto:Chr...@fu...> Chr...@fu...> >> Sent: Mittwoch, 6. September 2023 12:18 >> To: General OpenMS discussion < <mailto:ope...@li...> ope...@li...> >> Subject: Re: [Open-ms-general] Question to Internal Calibration >> >> Hi Simon, >> >> the build-in default value of Rscript does not work in your case >> because in general KNIME does not provide the PATH environment to the >> nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration >> cannot find the Rscript executable and you must point to it >> manually. >> Depending on the system you are on, the location of the Rscript >> executable will differ. >> One easy way to find it, is to use the build-in search functionality >> of your operating system, i.e. the Windows Explorer, Nautilus, Finder >> etc. >> If you are familiar with the commandline, try where rscript (for >> Windows) or which Rscript (for Linux/Mac). This should give you the >> desired path, if the R programming language was properly installed on >> your system. >> If you run KNIME on Windows, you need to check the File Extension >> (override)` box, otherwise KNIME will complain that Rscript has an >> .exe extension see attached image. >> >> Hope this helps. >> >> Cheers >> Chris >> >> >> -- >> Dr. Chris Bielow >> >> Bioinformatics Solution Center (BSC) >> www.bsc.fu-berlin.de >> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room >> K21, 14195 Berlin >> Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de >> >> From: <mailto:sim...@un...> sim...@un... < <mailto:sim...@un...> sim...@un...> >> Sent: Tuesday, September 5, 2023 1:16 PM >> To: <mailto:ope...@li...> ope...@li... >> Subject: [Open-ms-general] Question to Internal Calibration >> >> Dear customer service, >> I have a question regarding the internal calibration node. I >> personally prefer to work with OpenMS in the Knime platform. Now I >> stumbled over a problem with the internal calibration node in the >> Knimesoftware. The node in the OpenMS toppas is working fine because >> there the rscript execution is already embedded. For the node in >> the Knime platform this embedded rscript execution is missing and I >> must add an input file node with connection to the the calibration >> node. I cant find the rscript that is mentioned. >> >> I hope I write to the correct person to tackle that problem. If note >> maybe you can direct me to the right address or forum. >> Thanks in advance for your time and hopefully a answers to my >> question. >> >> Best Regards >> Simon Redlich >> _______________________________________________ >> Open-ms-general mailing list >> <mailto:Ope...@li...> Ope...@li... >> <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general > > -- > IPB is hiring: > * Researcher (PostDoc Cheminformatics) (m/f/d) > https://www.ipb-halle.de/en/career/job-vacancies/joboffer- > detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd > / > > Upcoming events: > * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe > <https://www.nfdi.de/cordi-2023/?lang=en> https://www.nfdi.de/cordi-2023/?lang=en > > * DGMet September 27th to 29th, 2023, Halle (Saale) > <https://dgmet.de/event/dgmet-annual-meeting/> https://dgmet.de/event/dgmet-annual-meeting/ > > * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld > https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 > > > --- > IPB Halle Computational Plant Biochemistry (CPB) > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 Tel. +49 (0) 345 5582 - 1470 > 06120 Halle +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > Open-ms-general mailing list > <mailto:Ope...@li...> Ope...@li... > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general > > > > _______________________________________________ > Open-ms-general mailing list > <mailto:Ope...@li...> Ope...@li... > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general > > > > _______________________________________________ > Open-ms-general mailing list > <mailto:Ope...@li...> Ope...@li... > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general -- Simon Redlich, Friedrich-Schiller-Universität Jena Institut for Anorganic and Analytical Chemistry Lessingstr. 8 07743 Jena Germany +493641(9)48288 _______________________________________________ Open-ms-general mailing list <mailto:Ope...@li...> Ope...@li... <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general |
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From: <sim...@un...> - 2023-10-27 10:58:28
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Hello Chris, I have a problem with the OpenMS 3.1.0-pre-nightly version. I tried to install the most of the available 3.1.0 versions from the website <https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/night ly/> https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightl y/ Up till version 2023-10-13 I could not manage to install it because something was missing. From Version 2023-10-16 on I was able to install it but the following message was shown for 1 sec: This application failed to start because it could not find or load the Qt platform plugin windows in . Reinstall the application may fix this problem The same problem was showing for all newer version and reinstalling it was not the solution. I tried it on two different PCs with windows without success. To the remark to the last part Ich hatte auch einen Screenshot in deinen GoogleDrive dateien gesehen fuer einen Labelfree Workflow von LC-MS Daten. Der waere aber fuer DirektInjection ungeeignet. Bin jetzt gerade nicht sicher warum dieser Workflow mit dabei war. I have the lablefree workflow in it because for some reason the workflow cant read the filename and gives me at the end a UNKNOWN for all samplenames in the Datasheet. The second Datasheet gives me the correct names. So I manually have to copy the sample names out of one datasheet into the one with my real data. Hope you understand. If not maybe we can talk in German. Maybe a additional problem that can be worked on as well to cancel out unnecessary nodes from the workflow. If necessary I can give you additional informations on the googledrive folder if this helps. Best regard Simon Hi Simon, I downloaded the data, looked at the problem and send you an email on Sept. 23rd. I copy it below (in german), for reference. Maybe it did not make it your inbox? Since I was at it now, I created a TOPPAS pipeline (attached) which 1) converts .Raw to mzmML 2) filters spectra based on RT range 3) merges whatever remains into a single MS1 spectrum. Some more annotation can be found in the workflow description when you open it in TOPPAS (see rightmost window named "Workflow Description" in TOPPAS). Hope this fits your needs. Feel free to get back in case something is unclear. cheers Chris ---- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de ----- Hi Simon, Ich bin vor meinem Urlaub nicht mehr dazu gekommen dir zu antworten: Der SpectraMerger hatte einen Bug und konnte nicht mit deinen Daten funktionieren. Das ist mittlerweile gefixt und unter https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightl y/ stehen tagesaktuelle Installationsdateien für verschiedene Betriebssysteme bereit. z.B. https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightl y/OpenMS-3.1.0-pre-nightly-latest-Win64.exe fuer Windows 10/11. Das sollte dein Problem loesen. Ich hatte auch einen Screenshot in deinen GoogleDrive dateien gesehen fuer einen Labelfree Workflow von LC-MS Daten. Der waere aber fuer DirektInjection ungeeignet. Bin jetzt gerade nicht sicher warum dieser Workflow mit dabei war. Ich bin noch eine Woche im Urlaub, danach kann ich mir das gerne noch mal genauer anschauen, wenn es Bedarf gibt. Vg Chris -- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de -----Original Message----- From: Simon Benjamin Redlich < <mailto:sim...@un...> sim...@un...> Sent: Thursday, October 19, 2023 11:04 AM To: General OpenMS discussion < <mailto:ope...@li...> ope...@li...> Subject: Re: [Open-ms-general] OpenMS Directinjection Hello Chris, are there any news about my request or did I overlooked a Email? I just noticed that Julianus Pfeuffer ask for permission for the googledrive folder. If there is no option to get the correct MS Data from the raw-Data without the xcalibur program, then we leave it like that. It just would be a dream to use just OpenMS for my pipeline. Best regard Simon Redlich Quoting <mailto:sim...@un...> sim...@un...: > Hi Chris, > sorry for the German. I can write it in English if you want. Steffen > sounded quite German so I thought it would be easier. Here the Link > <https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2> https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2 > Wk?usp=sharing > > Best Regards > Simon > > -----Original Message----- > From: Bielow, Chris < <mailto:Chr...@fu...> Chr...@fu...> > Sent: Freitag, 15. September 2023 14:35 > To: General OpenMS discussion < <mailto:ope...@li...> ope...@li...> > Subject: Re: [Open-ms-general] OpenMS Directinjection > > Hi Simon, > > the attachments did not arrive unfortunately. This may be due to the > way Sourceforge mailing lists are operated. > Can you upload the attachments, and ideally, the input mzML data that > you are trying to merge to some file upload service (e.g. > GoogleDrive, File.io, WeTransfer etc) and share the link here? > Alternatively you can open an issue on the OpenMS Github repository > and attach some files there. > Thanks! > > Cheers > Chris > > PS: could you solve your KNIME issue regarding MIME types? > > -- > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > -----Original Message----- > From: <mailto:sim...@un...> sim...@un... < <mailto:sim...@un...> sim...@un...> > Sent: Friday, September 15, 2023 2:15 PM > To: 'Neumann, Steffen' < <mailto:sne...@ip...> sne...@ip...>; 'General OpenMS > discussion' < <mailto:ope...@li...> ope...@li...> > Subject: [Open-ms-general] OpenMS Directinjection > > Hallo Steffen, > aufgrund deines Namens hoffe ich, dass ich auf deutsch mit dir > schreiben kann. Vielen Dank für deine Hilfe. > Mein nächstes Anliegen an dich ist eher ein Longshot, da ich nicht > weiß, wie gut du dich mit HR-MS auskennen. Ich versuche zur Zeit > mithilfe von OpenMS Direct Injectionen in tsv-Dateien umzuwandeln. > Mein Work-flow ist im ersten Bild zu sehen. Mein Ziel ist es die > centroid Daten (also Signale) unterschiedlichen Messungen in eine tsv > Datei zu kombieren. Bevor das aber passieren kann, muss ich zur Zeit > händisch jede Messung aufrufen und dort den gewünschten > Retentionszeibereich markieren um ein Massenspektrum mehrerer Scans zu > erhalten. Dieses Massenspektrum muss dann erneut als raw-Datei > exportiert werden. Dazu benötige ich Xcalibur (QualBrowser) von > ThermoFisher (wie sie in Bild 2 zu sehen ist). Die neu erstellten > raw-Dateien kann dann OpenMS ohne Probleme lesen, zur mzML-Datei > umwandeln und in einer tsv-Datei kombinieren. Die Bilder sind in der > Powerpoint enthalten > > Ich würde gerne OpenMS dazu nutzen mir diesen manuellen Teil > abzunehmen. Ich denke, dass der SpectraMerger mithilfe der > Block_method da weiterhelfen könnte. Leider kommt jedesmal der Fehler: > " Error: Unexpected internal error (the given size was not > expected: 0)". Leider schaffe ich es nicht diesen Fehler zu beheben. > Außerdem wird mir die Fehlermeldung: > " TOPPBase.cpp(1634): Error occurred in line 134 of file > E:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\t > opp\SpectraMerger.cpp (in function: enum OpenMS::TOPPBase::ExitCodes __cdecl TOPPSpectraMerger::main_(int,const char **)) !" ausgegeben wenn ich Debug aktiviere. Vielleicht hilft es ja. > > Ich kenne mich leider nur geringfügig mit Informatik aus und kann > damit wenig anfangen. > Falls du eine Möglichkeit kennst das zu beheben oder eine andere > Möglichkeit kennst mein Ziel mit openMS zu erreichen, auch gerne mit > anderen Nodes, dann würde ich mich sehr freuen und wäre dir sehr > dankbar, da dadurch mein Workflow deutlich schlanker werden würde. > Dadurch wird meine geplante Publikation übersichtlicher und wäre zu > 100% open source. > Ich hoffe du verstehst meine Probleme und mein Anliegen. > Falls du mir nicht weiterhelfen kannst, möchte ich trotzdem bei dir > für die investierte Zeit bedanken. > > Mit freundlichen Grüßen > Simon Redlich > > > -----Original Message----- > From: Neumann, Steffen < <mailto:sne...@ip...> sne...@ip...> > Sent: Donnerstag, 7. September 2023 17:25 > To: <mailto:ope...@li...> ope...@li... > Subject: Re: [Open-ms-general] Question to Internal Calibration > > Hi, > > side-comment: if the path to rscript.exe includes the R version, > you'll likely have to change that in case you update R and remove the > old version of R, or the Knome node will stop working. Unless you want > to install multiple versions of R, you could install it into a path > without version. > > As I don't know Windows and not too much Knime, I can't help with the > other problem. > > Another side comment: instead of the customer support, you are > reaching here the developers, power users and generally helpful OpenMS > community > :-) > > Grüsse nach Jena, > Yours, > Steffen > > > > > On Thu, 2023-09-07 at 13:24 +0200, <mailto:sim...@un...> sim...@un... wrote: >> Hello Chris, >> thank for your fast respond. >> I found the rscript.exe but if I check the File Extension (override)- >> box and keep it empty like in your picture KNIME starts to show the >> problem invalid settings: no file extension (override) provided. No >> matter what I type in the box as alternative extension its not what >> the node wants to have. So, in summary: I could figure out some of my >> problems but Im still stuck and cant run the node. >> >> Best regards Simon >> >> From: Bielow, Chris < <mailto:Chr...@fu...> Chr...@fu...> >> Sent: Mittwoch, 6. September 2023 12:18 >> To: General OpenMS discussion < <mailto:ope...@li...> ope...@li...> >> Subject: Re: [Open-ms-general] Question to Internal Calibration >> >> Hi Simon, >> >> the build-in default value of Rscript does not work in your case >> because in general KNIME does not provide the PATH environment to the >> nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration >> cannot find the Rscript executable and you must point to it >> manually. >> Depending on the system you are on, the location of the Rscript >> executable will differ. >> One easy way to find it, is to use the build-in search functionality >> of your operating system, i.e. the Windows Explorer, Nautilus, Finder >> etc. >> If you are familiar with the commandline, try where rscript (for >> Windows) or which Rscript (for Linux/Mac). This should give you the >> desired path, if the R programming language was properly installed on >> your system. >> If you run KNIME on Windows, you need to check the File Extension >> (override)` box, otherwise KNIME will complain that Rscript has an >> .exe extension see attached image. >> >> Hope this helps. >> >> Cheers >> Chris >> >> >> -- >> Dr. Chris Bielow >> >> Bioinformatics Solution Center (BSC) >> www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> >> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room >> K21, 14195 Berlin >> Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de >> >> From: <mailto:sim...@un...> sim...@un... < <mailto:sim...@un...> sim...@un...> >> Sent: Tuesday, September 5, 2023 1:16 PM >> To: <mailto:ope...@li...> ope...@li... >> Subject: [Open-ms-general] Question to Internal Calibration >> >> Dear customer service, >> I have a question regarding the internal calibration node. I >> personally prefer to work with OpenMS in the Knime platform. Now I >> stumbled over a problem with the internal calibration node in the >> Knimesoftware. The node in the OpenMS toppas is working fine because >> there the rscript execution is already embedded. For the node in >> the Knime platform this embedded rscript execution is missing and I >> must add an input file node with connection to the the calibration >> node. I cant find the rscript that is mentioned. >> >> I hope I write to the correct person to tackle that problem. If note >> maybe you can direct me to the right address or forum. >> Thanks in advance for your time and hopefully a answers to my >> question. >> >> Best Regards >> Simon Redlich >> _______________________________________________ >> Open-ms-general mailing list >> <mailto:Ope...@li...> Ope...@li... >> <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general > > -- > IPB is hiring: > * Researcher (PostDoc Cheminformatics) (m/f/d) > https://www.ipb-halle.de/en/career/job-vacancies/joboffer- > detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd > / > > Upcoming events: > * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe > <https://www.nfdi.de/cordi-2023/?lang=en> https://www.nfdi.de/cordi-2023/?lang=en > > * DGMet September 27th to 29th, 2023, Halle (Saale) > <https://dgmet.de/event/dgmet-annual-meeting/> https://dgmet.de/event/dgmet-annual-meeting/ > > * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld > https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 > > > --- > IPB Halle Computational Plant Biochemistry (CPB) > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 Tel. +49 (0) 345 5582 - 1470 > 06120 Halle +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > Open-ms-general mailing list > <mailto:Ope...@li...> Ope...@li... > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general > > > > _______________________________________________ > Open-ms-general mailing list > <mailto:Ope...@li...> Ope...@li... > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general > > > > _______________________________________________ > Open-ms-general mailing list > <mailto:Ope...@li...> Ope...@li... > <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general -- Simon Redlich, Friedrich-Schiller-Universität Jena Institut for Anorganic and Analytical Chemistry Lessingstr. 8 07743 Jena Germany +493641(9)48288 _______________________________________________ Open-ms-general mailing list <mailto:Ope...@li...> Ope...@li... <https://lists.sourceforge.net/lists/listinfo/open-ms-general> https://lists.sourceforge.net/lists/listinfo/open-ms-general |
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From: Bielow, C. <Chr...@fu...> - 2023-10-19 11:21:23
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Hi Simon, I downloaded the data, looked at the problem and send you an email on Sept. 23rd. I copy it below (in german), for reference. Maybe it did not make it your inbox? Since I was at it now, I created a TOPPAS pipeline (attached) which 1) converts .Raw to mzmML 2) filters spectra based on RT range 3) merges whatever remains into a single MS1 spectrum. Some more annotation can be found in the workflow description when you open it in TOPPAS (see rightmost window named "Workflow Description" in TOPPAS). Hope this fits your needs. Feel free to get back in case something is unclear. cheers Chris ---- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de ----- Hi Simon, Ich bin vor meinem Urlaub nicht mehr dazu gekommen dir zu antworten: Der SpectraMerger hatte einen Bug und konnte nicht mit deinen Daten funktionieren. Das ist mittlerweile gefixt und unter https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/ stehen tagesaktuelle Installationsdateien für verschiedene Betriebssysteme bereit. z.B. https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/OpenMS-3.1.0-pre-nightly-latest-Win64.exe fuer Windows 10/11. Das sollte dein Problem loesen. Ich hatte auch einen Screenshot in deinen GoogleDrive dateien gesehen fuer einen Labelfree Workflow von LC-MS Daten. Der waere aber fuer DirektInjection ungeeignet. Bin jetzt gerade nicht sicher warum dieser Workflow mit dabei war. Ich bin noch eine Woche im Urlaub, danach kann ich mir das gerne noch mal genauer anschauen, wenn es Bedarf gibt. Vg Chris -- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de -----Original Message----- From: Simon Benjamin Redlich <sim...@un...> Sent: Thursday, October 19, 2023 11:04 AM To: General OpenMS discussion <ope...@li...> Subject: Re: [Open-ms-general] OpenMS Directinjection Hello Chris, are there any news about my request or did I overlooked a Email? I just noticed that Julianus Pfeuffer ask for permission for the googledrive folder. If there is no option to get the correct MS Data from the raw-Data without the xcalibur program, then we leave it like that. It just would be a dream to use just OpenMS for my pipeline. Best regard Simon Redlich Quoting sim...@un...: > Hi Chris, > sorry for the German. I can write it in English if you want. Steffen > sounded quite German so I thought it would be easier. Here the Link > https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2 > Wk?usp=sharing > > Best Regards > Simon > > -----Original Message----- > From: Bielow, Chris <Chr...@fu...> > Sent: Freitag, 15. September 2023 14:35 > To: General OpenMS discussion <ope...@li...> > Subject: Re: [Open-ms-general] OpenMS Directinjection > > Hi Simon, > > the attachments did not arrive unfortunately. This may be due to the > way Sourceforge mailing lists are operated. > Can you upload the attachments, and ideally, the input mzML data that > you are trying to merge to some file upload service (e.g. > GoogleDrive, File.io, WeTransfer etc) and share the link here? > Alternatively you can open an issue on the OpenMS Github repository > and attach some files there. > Thanks! > > Cheers > Chris > > PS: could you solve your KNIME issue regarding MIME types? > > -- > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > www.bsc.fu-berlin.de > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > -----Original Message----- > From: sim...@un... <sim...@un...> > Sent: Friday, September 15, 2023 2:15 PM > To: 'Neumann, Steffen' <sne...@ip...>; 'General OpenMS > discussion' <ope...@li...> > Subject: [Open-ms-general] OpenMS Directinjection > > Hallo Steffen, > aufgrund deines Namens hoffe ich, dass ich auf deutsch mit dir > schreiben kann. Vielen Dank für deine Hilfe. > Mein nächstes Anliegen an dich ist eher ein Longshot, da ich nicht > weiß, wie gut du dich mit HR-MS auskennen. Ich versuche zur Zeit > mithilfe von OpenMS Direct Injectionen in tsv-Dateien umzuwandeln. > Mein Work-flow ist im ersten Bild zu sehen. Mein Ziel ist es die > centroid Daten (also Signale) unterschiedlichen Messungen in eine tsv > Datei zu kombieren. Bevor das aber passieren kann, muss ich zur Zeit > händisch jede Messung aufrufen und dort den gewünschten > Retentionszeibereich markieren um ein Massenspektrum mehrerer Scans zu > erhalten. Dieses Massenspektrum muss dann erneut als raw-Datei > exportiert werden. Dazu benötige ich Xcalibur (QualBrowser) von > ThermoFisher (wie sie in Bild 2 zu sehen ist). Die neu erstellten > raw-Dateien kann dann OpenMS ohne Probleme lesen, zur mzML-Datei > umwandeln und in einer tsv-Datei kombinieren. Die Bilder sind in der > Powerpoint enthalten > > Ich würde gerne OpenMS dazu nutzen mir diesen manuellen Teil > abzunehmen. Ich denke, dass der SpectraMerger mithilfe der > Block_method da weiterhelfen könnte. Leider kommt jedesmal der Fehler: > " Error: Unexpected internal error (the given size was not > expected: 0)". Leider schaffe ich es nicht diesen Fehler zu beheben. > Außerdem wird mir die Fehlermeldung: > " TOPPBase.cpp(1634): Error occurred in line 134 of file > E:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\t > opp\SpectraMerger.cpp (in function: enum OpenMS::TOPPBase::ExitCodes __cdecl TOPPSpectraMerger::main_(int,const char **)) !" ausgegeben wenn ich Debug aktiviere. Vielleicht hilft es ja. > > Ich kenne mich leider nur geringfügig mit Informatik aus und kann > damit wenig anfangen. > Falls du eine Möglichkeit kennst das zu beheben oder eine andere > Möglichkeit kennst mein Ziel mit openMS zu erreichen, auch gerne mit > anderen Nodes, dann würde ich mich sehr freuen und wäre dir sehr > dankbar, da dadurch mein Workflow deutlich schlanker werden würde. > Dadurch wird meine geplante Publikation übersichtlicher und wäre zu > 100% open source. > Ich hoffe du verstehst meine Probleme und mein Anliegen. > Falls du mir nicht weiterhelfen kannst, möchte ich trotzdem bei dir > für die investierte Zeit bedanken. > > Mit freundlichen Grüßen > Simon Redlich > > > -----Original Message----- > From: Neumann, Steffen <sne...@ip...> > Sent: Donnerstag, 7. September 2023 17:25 > To: ope...@li... > Subject: Re: [Open-ms-general] Question to Internal Calibration > > Hi, > > side-comment: if the path to rscript.exe includes the R version, > you'll likely have to change that in case you update R and remove the > old version of R, or the Knome node will stop working. Unless you want > to install multiple versions of R, you could install it into a path > without version. > > As I don't know Windows and not too much Knime, I can't help with the > other problem. > > Another side comment: instead of the customer support, you are > reaching here the developers, power users and generally helpful OpenMS > community > :-) > > Grüsse nach Jena, > Yours, > Steffen > > > > > On Thu, 2023-09-07 at 13:24 +0200, sim...@un... wrote: >> Hello Chris, >> thank for your fast respond. >> I found the rscript.exe but if I check the File Extension (override)- >> box and keep it empty like in your picture KNIME starts to show the >> problem “invalid settings: no file extension (override) provided. No >> matter what I type in the box as alternative extension its not what >> the node wants to have. So, in summary: I could figure out some of my >> problems but I’m still stuck and can’t run the node. >> >> Best regards Simon >> >> From: Bielow, Chris <Chr...@fu...> >> Sent: Mittwoch, 6. September 2023 12:18 >> To: General OpenMS discussion <ope...@li...> >> Subject: Re: [Open-ms-general] Question to Internal Calibration >> >> Hi Simon, >> >> the build-in default value of ‚Rscript‘ does not work in your case >> because in general KNIME does not provide the PATH environment to the >> nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration >> cannot find the ‘Rscript’ executable and you must point to it >> manually. >> Depending on the system you are on, the location of the ‘Rscript’ >> executable will differ. >> One easy way to find it, is to use the build-in search functionality >> of your operating system, i.e. the Windows Explorer, Nautilus, Finder >> etc. >> If you are familiar with the commandline, try “where rscript” (for >> Windows) or “which Rscript” (for Linux/Mac). This should give you the >> desired path, if the R programming language was properly installed on >> your system. >> If you run KNIME on Windows, you need to check the ‘File Extension >> (override)` box, otherwise KNIME will complain that Rscript has an >> ‘.exe’ extension – see attached image. >> >> Hope this helps. >> >> Cheers >> Chris >> >> >> -- >> Dr. Chris Bielow >> >> Bioinformatics Solution Center (BSC) >> www.bsc.fu-berlin.de >> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room >> K21, 14195 Berlin >> Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de >> >> From: sim...@un... <sim...@un...> >> Sent: Tuesday, September 5, 2023 1:16 PM >> To: ope...@li... >> Subject: [Open-ms-general] Question to Internal Calibration >> >> Dear customer service, >> I have a question regarding the internal calibration node. I >> personally prefer to work with OpenMS in the Knime platform. Now I >> stumbled over a problem with the internal calibration node in the >> Knimesoftware. The node in the OpenMS toppas is working fine because >> there the “rscript execution” is already embedded. For the node in >> the Knime platform this embedded “rscript execution” is missing and I >> must add an input file node with connection to the the calibration >> node. I cant find the rscript that is mentioned. >> >> I hope I write to the correct person to tackle that problem. If note >> maybe you can direct me to the right address or forum. >> Thanks in advance for your time and hopefully a answers to my >> question. >> >> Best Regards >> Simon Redlich >> _______________________________________________ >> Open-ms-general mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/open-ms-general > > -- > IPB is hiring: > * Researcher (PostDoc Cheminformatics) (m/f/d) > https://www.ipb-halle.de/en/career/job-vacancies/joboffer- > detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd > / > > Upcoming events: > * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe > https://www.nfdi.de/cordi-2023/?lang=en > > * DGMet September 27th to 29th, 2023, Halle (Saale) > https://dgmet.de/event/dgmet-annual-meeting/ > > * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld > https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 > > > --- > IPB Halle Computational Plant Biochemistry (CPB) > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 Tel. +49 (0) 345 5582 - 1470 > 06120 Halle +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general > > > > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general > > > > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general -- Simon Redlich, Friedrich-Schiller-Universität Jena Institut for Anorganic and Analytical Chemistry Lessingstr. 8 07743 Jena Germany +493641(9)48288 _______________________________________________ Open-ms-general mailing list Ope...@li... https://lists.sourceforge.net/lists/listinfo/open-ms-general |
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From: Simon B. R. <sim...@un...> - 2023-10-19 09:04:04
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Hello Chris, are there any news about my request or did I overlooked a Email? I just noticed that Julianus Pfeuffer ask for permission for the googledrive folder. If there is no option to get the correct MS Data from the raw-Data without the xcalibur program, then we leave it like that. It just would be a dream to use just OpenMS for my pipeline. Best regard Simon Redlich Quoting sim...@un...: > Hi Chris, > sorry for the German. I can write it in English if you want. Steffen > sounded quite German so I thought it would be easier. Here the Link > https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2Wk?usp=sharing > > Best Regards > Simon > > -----Original Message----- > From: Bielow, Chris <Chr...@fu...> > Sent: Freitag, 15. September 2023 14:35 > To: General OpenMS discussion <ope...@li...> > Subject: Re: [Open-ms-general] OpenMS Directinjection > > Hi Simon, > > the attachments did not arrive unfortunately. This may be due to the > way Sourceforge mailing lists are operated. > Can you upload the attachments, and ideally, the input mzML data > that you are trying to merge to some file upload service (e.g. > GoogleDrive, File.io, WeTransfer etc) and share the link here? > Alternatively you can open an issue on the OpenMS Github repository > and attach some files there. > Thanks! > > Cheers > Chris > > PS: could you solve your KNIME issue regarding MIME types? > > -- > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > www.bsc.fu-berlin.de > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > -----Original Message----- > From: sim...@un... <sim...@un...> > Sent: Friday, September 15, 2023 2:15 PM > To: 'Neumann, Steffen' <sne...@ip...>; 'General OpenMS > discussion' <ope...@li...> > Subject: [Open-ms-general] OpenMS Directinjection > > Hallo Steffen, > aufgrund deines Namens hoffe ich, dass ich auf deutsch mit dir > schreiben kann. Vielen Dank für deine Hilfe. > Mein nächstes Anliegen an dich ist eher ein Longshot, da ich nicht > weiß, wie gut du dich mit HR-MS auskennen. Ich versuche zur Zeit > mithilfe von OpenMS Direct Injectionen in tsv-Dateien umzuwandeln. > Mein Work-flow ist im ersten Bild zu sehen. Mein Ziel ist es die > centroid Daten (also Signale) unterschiedlichen Messungen in eine > tsv Datei zu kombieren. Bevor das aber passieren kann, muss ich zur > Zeit händisch jede Messung aufrufen und dort den gewünschten > Retentionszeibereich markieren um ein Massenspektrum mehrerer Scans > zu erhalten. Dieses Massenspektrum muss dann erneut als raw-Datei > exportiert werden. Dazu benötige ich Xcalibur (QualBrowser) von > ThermoFisher (wie sie in Bild 2 zu sehen ist). Die neu erstellten > raw-Dateien kann dann OpenMS ohne Probleme lesen, zur mzML-Datei > umwandeln und in einer tsv-Datei kombinieren. Die Bilder sind in der > Powerpoint enthalten > > Ich würde gerne OpenMS dazu nutzen mir diesen manuellen Teil > abzunehmen. Ich denke, dass der SpectraMerger mithilfe der > Block_method da weiterhelfen könnte. Leider kommt jedesmal der Fehler: > " Error: Unexpected internal error (the given size was not > expected: 0)". Leider schaffe ich es nicht diesen Fehler zu beheben. > Außerdem wird mir die Fehlermeldung: > " TOPPBase.cpp(1634): Error occurred in line 134 of file > E:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\topp\SpectraMerger.cpp (in function: enum OpenMS::TOPPBase::ExitCodes __cdecl TOPPSpectraMerger::main_(int,const char **)) !" ausgegeben wenn ich Debug aktiviere. Vielleicht hilft es > ja. > > Ich kenne mich leider nur geringfügig mit Informatik aus und kann > damit wenig anfangen. > Falls du eine Möglichkeit kennst das zu beheben oder eine andere > Möglichkeit kennst mein Ziel mit openMS zu erreichen, auch gerne mit > anderen Nodes, dann würde ich mich sehr freuen und wäre dir sehr > dankbar, da dadurch mein Workflow deutlich schlanker werden würde. > Dadurch wird meine geplante Publikation übersichtlicher und wäre zu > 100% open source. > Ich hoffe du verstehst meine Probleme und mein Anliegen. > Falls du mir nicht weiterhelfen kannst, möchte ich trotzdem bei dir > für die investierte Zeit bedanken. > > Mit freundlichen Grüßen > Simon Redlich > > > -----Original Message----- > From: Neumann, Steffen <sne...@ip...> > Sent: Donnerstag, 7. September 2023 17:25 > To: ope...@li... > Subject: Re: [Open-ms-general] Question to Internal Calibration > > Hi, > > side-comment: if the path to rscript.exe includes the R version, > you'll likely have to change that in case you update R and remove > the old version of R, or the Knome node will stop working. Unless > you want to install multiple versions of R, you could install it > into a path without version. > > As I don't know Windows and not too much Knime, I can't help with > the other problem. > > Another side comment: instead of the customer support, you are > reaching here the developers, power users and generally helpful > OpenMS community > :-) > > Grüsse nach Jena, > Yours, > Steffen > > > > > On Thu, 2023-09-07 at 13:24 +0200, sim...@un... wrote: >> Hello Chris, >> thank for your fast respond. >> I found the rscript.exe but if I check the File Extension (override)- >> box and keep it empty like in your picture KNIME starts to show the >> problem “invalid settings: no file extension (override) provided. No >> matter what I type in the box as alternative extension its not what >> the node wants to have. So, in summary: I could figure out some of my >> problems but I’m still stuck and can’t run the node. >> >> Best regards Simon >> >> From: Bielow, Chris <Chr...@fu...> >> Sent: Mittwoch, 6. September 2023 12:18 >> To: General OpenMS discussion <ope...@li...> >> Subject: Re: [Open-ms-general] Question to Internal Calibration >> >> Hi Simon, >> >> the build-in default value of ‚Rscript‘ does not work in your case >> because in general KNIME does not provide the PATH environment to the >> nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration >> cannot find the ‘Rscript’ executable and you must point to it >> manually. >> Depending on the system you are on, the location of the ‘Rscript’ >> executable will differ. >> One easy way to find it, is to use the build-in search functionality >> of your operating system, i.e. the Windows Explorer, Nautilus, Finder >> etc. >> If you are familiar with the commandline, try “where rscript” (for >> Windows) or “which Rscript” (for Linux/Mac). This should give you the >> desired path, if the R programming language was properly installed on >> your system. >> If you run KNIME on Windows, you need to check the ‘File Extension >> (override)` box, otherwise KNIME will complain that Rscript has an >> ‘.exe’ extension – see attached image. >> >> Hope this helps. >> >> Cheers >> Chris >> >> >> -- >> Dr. Chris Bielow >> >> Bioinformatics Solution Center (BSC) >> www.bsc.fu-berlin.de >> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room >> K21, 14195 Berlin >> Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de >> >> From: sim...@un... <sim...@un...> >> Sent: Tuesday, September 5, 2023 1:16 PM >> To: ope...@li... >> Subject: [Open-ms-general] Question to Internal Calibration >> >> Dear customer service, >> I have a question regarding the internal calibration node. I >> personally prefer to work with OpenMS in the Knime platform. Now I >> stumbled over a problem with the internal calibration node in the >> Knimesoftware. The node in the OpenMS toppas is working fine because >> there the “rscript execution” is already embedded. For the node in the >> Knime platform this embedded “rscript execution” is missing and I must >> add an input file node with connection to the the calibration node. I >> cant find the rscript that is mentioned. >> >> I hope I write to the correct person to tackle that problem. If note >> maybe you can direct me to the right address or forum. >> Thanks in advance for your time and hopefully a answers to my >> question. >> >> Best Regards >> Simon Redlich >> _______________________________________________ >> Open-ms-general mailing list >> Ope...@li... >> https://lists.sourceforge.net/lists/listinfo/open-ms-general > > -- > IPB is hiring: > * Researcher (PostDoc Cheminformatics) (m/f/d) > https://www.ipb-halle.de/en/career/job-vacancies/joboffer- > detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd/ > > Upcoming events: > * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe > https://www.nfdi.de/cordi-2023/?lang=en > > * DGMet September 27th to 29th, 2023, Halle (Saale) > https://dgmet.de/event/dgmet-annual-meeting/ > > * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld > https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 > > > --- > IPB Halle Computational Plant Biochemistry (CPB) > Dr. Steffen Neumann http://www.IPB-Halle.DE > Weinberg 3 Tel. +49 (0) 345 5582 - 1470 > 06120 Halle +49 (0) 345 5582 - 0 > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general > > > > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general > > > > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general -- Simon Redlich, Friedrich-Schiller-Universität Jena Institut for Anorganic and Analytical Chemistry Lessingstr. 8 07743 Jena Germany +493641(9)48288 |
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From: <sim...@un...> - 2023-09-15 12:50:07
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Hi Chris, sorry for the German. I can write it in English if you want. Steffen sounded quite German so I thought it would be easier. Here the Link https://drive.google.com/drive/folders/11cxKms0zUQVTWsTz8RuV8Zr-ContZ2Wk?usp=sharing Best Regards Simon -----Original Message----- From: Bielow, Chris <Chr...@fu...> Sent: Freitag, 15. September 2023 14:35 To: General OpenMS discussion <ope...@li...> Subject: Re: [Open-ms-general] OpenMS Directinjection Hi Simon, the attachments did not arrive unfortunately. This may be due to the way Sourceforge mailing lists are operated. Can you upload the attachments, and ideally, the input mzML data that you are trying to merge to some file upload service (e.g. GoogleDrive, File.io, WeTransfer etc) and share the link here? Alternatively you can open an issue on the OpenMS Github repository and attach some files there. Thanks! Cheers Chris PS: could you solve your KNIME issue regarding MIME types? -- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de -----Original Message----- From: sim...@un... <sim...@un...> Sent: Friday, September 15, 2023 2:15 PM To: 'Neumann, Steffen' <sne...@ip...>; 'General OpenMS discussion' <ope...@li...> Subject: [Open-ms-general] OpenMS Directinjection Hallo Steffen, aufgrund deines Namens hoffe ich, dass ich auf deutsch mit dir schreiben kann. Vielen Dank für deine Hilfe. Mein nächstes Anliegen an dich ist eher ein Longshot, da ich nicht weiß, wie gut du dich mit HR-MS auskennen. Ich versuche zur Zeit mithilfe von OpenMS Direct Injectionen in tsv-Dateien umzuwandeln. Mein Work-flow ist im ersten Bild zu sehen. Mein Ziel ist es die centroid Daten (also Signale) unterschiedlichen Messungen in eine tsv Datei zu kombieren. Bevor das aber passieren kann, muss ich zur Zeit händisch jede Messung aufrufen und dort den gewünschten Retentionszeibereich markieren um ein Massenspektrum mehrerer Scans zu erhalten. Dieses Massenspektrum muss dann erneut als raw-Datei exportiert werden. Dazu benötige ich Xcalibur (QualBrowser) von ThermoFisher (wie sie in Bild 2 zu sehen ist). Die neu erstellten raw-Dateien kann dann OpenMS ohne Probleme lesen, zur mzML-Datei umwandeln und in einer tsv-Datei kombinieren. Die Bilder sind in der Powerpoint enthalten Ich würde gerne OpenMS dazu nutzen mir diesen manuellen Teil abzunehmen. Ich denke, dass der SpectraMerger mithilfe der Block_method da weiterhelfen könnte. Leider kommt jedesmal der Fehler: " Error: Unexpected internal error (the given size was not expected: 0)". Leider schaffe ich es nicht diesen Fehler zu beheben. Außerdem wird mir die Fehlermeldung: " TOPPBase.cpp(1634): Error occurred in line 134 of file E:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\topp\SpectraMerger.cpp (in function: enum OpenMS::TOPPBase::ExitCodes __cdecl TOPPSpectraMerger::main_(int,const char **)) !" ausgegeben wenn ich Debug aktiviere. Vielleicht hilft es ja. Ich kenne mich leider nur geringfügig mit Informatik aus und kann damit wenig anfangen. Falls du eine Möglichkeit kennst das zu beheben oder eine andere Möglichkeit kennst mein Ziel mit openMS zu erreichen, auch gerne mit anderen Nodes, dann würde ich mich sehr freuen und wäre dir sehr dankbar, da dadurch mein Workflow deutlich schlanker werden würde. Dadurch wird meine geplante Publikation übersichtlicher und wäre zu 100% open source. Ich hoffe du verstehst meine Probleme und mein Anliegen. Falls du mir nicht weiterhelfen kannst, möchte ich trotzdem bei dir für die investierte Zeit bedanken. Mit freundlichen Grüßen Simon Redlich -----Original Message----- From: Neumann, Steffen <sne...@ip...> Sent: Donnerstag, 7. September 2023 17:25 To: ope...@li... Subject: Re: [Open-ms-general] Question to Internal Calibration Hi, side-comment: if the path to rscript.exe includes the R version, you'll likely have to change that in case you update R and remove the old version of R, or the Knome node will stop working. Unless you want to install multiple versions of R, you could install it into a path without version. As I don't know Windows and not too much Knime, I can't help with the other problem. Another side comment: instead of the customer support, you are reaching here the developers, power users and generally helpful OpenMS community :-) Grüsse nach Jena, Yours, Steffen On Thu, 2023-09-07 at 13:24 +0200, sim...@un... wrote: > Hello Chris, > thank for your fast respond. > I found the rscript.exe but if I check the File Extension (override)- > box and keep it empty like in your picture KNIME starts to show the > problem “invalid settings: no file extension (override) provided. No > matter what I type in the box as alternative extension its not what > the node wants to have. So, in summary: I could figure out some of my > problems but I’m still stuck and can’t run the node. > > Best regards Simon > > From: Bielow, Chris <Chr...@fu...> > Sent: Mittwoch, 6. September 2023 12:18 > To: General OpenMS discussion <ope...@li...> > Subject: Re: [Open-ms-general] Question to Internal Calibration > > Hi Simon, > > the build-in default value of ‚Rscript‘ does not work in your case > because in general KNIME does not provide the PATH environment to the > nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration > cannot find the ‘Rscript’ executable and you must point to it > manually. > Depending on the system you are on, the location of the ‘Rscript’ > executable will differ. > One easy way to find it, is to use the build-in search functionality > of your operating system, i.e. the Windows Explorer, Nautilus, Finder > etc. > If you are familiar with the commandline, try “where rscript” (for > Windows) or “which Rscript” (for Linux/Mac). This should give you the > desired path, if the R programming language was properly installed on > your system. > If you run KNIME on Windows, you need to check the ‘File Extension > (override)` box, otherwise KNIME will complain that Rscript has an > ‘.exe’ extension – see attached image. > > Hope this helps. > > Cheers > Chris > > > -- > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > www.bsc.fu-berlin.de > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > From: sim...@un... <sim...@un...> > Sent: Tuesday, September 5, 2023 1:16 PM > To: ope...@li... > Subject: [Open-ms-general] Question to Internal Calibration > > Dear customer service, > I have a question regarding the internal calibration node. I > personally prefer to work with OpenMS in the Knime platform. Now I > stumbled over a problem with the internal calibration node in the > Knimesoftware. The node in the OpenMS toppas is working fine because > there the “rscript execution” is already embedded. For the node in the > Knime platform this embedded “rscript execution” is missing and I must > add an input file node with connection to the the calibration node. I > cant find the rscript that is mentioned. > > I hope I write to the correct person to tackle that problem. If note > maybe you can direct me to the right address or forum. > Thanks in advance for your time and hopefully a answers to my > question. > > Best Regards > Simon Redlich > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general -- IPB is hiring: * Researcher (PostDoc Cheminformatics) (m/f/d) https://www.ipb-halle.de/en/career/job-vacancies/joboffer- detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd/ Upcoming events: * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe https://www.nfdi.de/cordi-2023/?lang=en * DGMet September 27th to 29th, 2023, Halle (Saale) https://dgmet.de/event/dgmet-annual-meeting/ * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 --- IPB Halle Computational Plant Biochemistry (CPB) Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Open-ms-general mailing list Ope...@li... https://lists.sourceforge.net/lists/listinfo/open-ms-general _______________________________________________ Open-ms-general mailing list Ope...@li... https://lists.sourceforge.net/lists/listinfo/open-ms-general |
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From: Bielow, C. <Chr...@fu...> - 2023-09-15 12:35:16
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Hi Simon, the attachments did not arrive unfortunately. This may be due to the way Sourceforge mailing lists are operated. Can you upload the attachments, and ideally, the input mzML data that you are trying to merge to some file upload service (e.g. GoogleDrive, File.io, WeTransfer etc) and share the link here? Alternatively you can open an issue on the OpenMS Github repository and attach some files there. Thanks! Cheers Chris PS: could you solve your KNIME issue regarding MIME types? -- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de -----Original Message----- From: sim...@un... <sim...@un...> Sent: Friday, September 15, 2023 2:15 PM To: 'Neumann, Steffen' <sne...@ip...>; 'General OpenMS discussion' <ope...@li...> Subject: [Open-ms-general] OpenMS Directinjection Hallo Steffen, aufgrund deines Namens hoffe ich, dass ich auf deutsch mit dir schreiben kann. Vielen Dank für deine Hilfe. Mein nächstes Anliegen an dich ist eher ein Longshot, da ich nicht weiß, wie gut du dich mit HR-MS auskennen. Ich versuche zur Zeit mithilfe von OpenMS Direct Injectionen in tsv-Dateien umzuwandeln. Mein Work-flow ist im ersten Bild zu sehen. Mein Ziel ist es die centroid Daten (also Signale) unterschiedlichen Messungen in eine tsv Datei zu kombieren. Bevor das aber passieren kann, muss ich zur Zeit händisch jede Messung aufrufen und dort den gewünschten Retentionszeibereich markieren um ein Massenspektrum mehrerer Scans zu erhalten. Dieses Massenspektrum muss dann erneut als raw-Datei exportiert werden. Dazu benötige ich Xcalibur (QualBrowser) von ThermoFisher (wie sie in Bild 2 zu sehen ist). Die neu erstellten raw-Dateien kann dann OpenMS ohne Probleme lesen, zur mzML-Datei umwandeln und in einer tsv-Datei kombinieren. Die Bilder sind in der Powerpoint enthalten Ich würde gerne OpenMS dazu nutzen mir diesen manuellen Teil abzunehmen. Ich denke, dass der SpectraMerger mithilfe der Block_method da weiterhelfen könnte. Leider kommt jedesmal der Fehler: " Error: Unexpected internal error (the given size was not expected: 0)". Leider schaffe ich es nicht diesen Fehler zu beheben. Außerdem wird mir die Fehlermeldung: " TOPPBase.cpp(1634): Error occurred in line 134 of file E:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\topp\SpectraMerger.cpp (in function: enum OpenMS::TOPPBase::ExitCodes __cdecl TOPPSpectraMerger::main_(int,const char **)) !" ausgegeben wenn ich Debug aktiviere. Vielleicht hilft es ja. Ich kenne mich leider nur geringfügig mit Informatik aus und kann damit wenig anfangen. Falls du eine Möglichkeit kennst das zu beheben oder eine andere Möglichkeit kennst mein Ziel mit openMS zu erreichen, auch gerne mit anderen Nodes, dann würde ich mich sehr freuen und wäre dir sehr dankbar, da dadurch mein Workflow deutlich schlanker werden würde. Dadurch wird meine geplante Publikation übersichtlicher und wäre zu 100% open source. Ich hoffe du verstehst meine Probleme und mein Anliegen. Falls du mir nicht weiterhelfen kannst, möchte ich trotzdem bei dir für die investierte Zeit bedanken. Mit freundlichen Grüßen Simon Redlich -----Original Message----- From: Neumann, Steffen <sne...@ip...> Sent: Donnerstag, 7. September 2023 17:25 To: ope...@li... Subject: Re: [Open-ms-general] Question to Internal Calibration Hi, side-comment: if the path to rscript.exe includes the R version, you'll likely have to change that in case you update R and remove the old version of R, or the Knome node will stop working. Unless you want to install multiple versions of R, you could install it into a path without version. As I don't know Windows and not too much Knime, I can't help with the other problem. Another side comment: instead of the customer support, you are reaching here the developers, power users and generally helpful OpenMS community :-) Grüsse nach Jena, Yours, Steffen On Thu, 2023-09-07 at 13:24 +0200, sim...@un... wrote: > Hello Chris, > thank for your fast respond. > I found the rscript.exe but if I check the File Extension (override)- > box and keep it empty like in your picture KNIME starts to show the > problem “invalid settings: no file extension (override) provided. No > matter what I type in the box as alternative extension its not what > the node wants to have. So, in summary: I could figure out some of my > problems but I’m still stuck and can’t run the node. > > Best regards Simon > > From: Bielow, Chris <Chr...@fu...> > Sent: Mittwoch, 6. September 2023 12:18 > To: General OpenMS discussion <ope...@li...> > Subject: Re: [Open-ms-general] Question to Internal Calibration > > Hi Simon, > > the build-in default value of ‚Rscript‘ does not work in your case > because in general KNIME does not provide the PATH environment to the > nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration > cannot find the ‘Rscript’ executable and you must point to it > manually. > Depending on the system you are on, the location of the ‘Rscript’ > executable will differ. > One easy way to find it, is to use the build-in search functionality > of your operating system, i.e. the Windows Explorer, Nautilus, Finder > etc. > If you are familiar with the commandline, try “where rscript” (for > Windows) or “which Rscript” (for Linux/Mac). This should give you the > desired path, if the R programming language was properly installed on > your system. > If you run KNIME on Windows, you need to check the ‘File Extension > (override)` box, otherwise KNIME will complain that Rscript has an > ‘.exe’ extension – see attached image. > > Hope this helps. > > Cheers > Chris > > > -- > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > www.bsc.fu-berlin.de > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > From: sim...@un... <sim...@un...> > Sent: Tuesday, September 5, 2023 1:16 PM > To: ope...@li... > Subject: [Open-ms-general] Question to Internal Calibration > > Dear customer service, > I have a question regarding the internal calibration node. I > personally prefer to work with OpenMS in the Knime platform. Now I > stumbled over a problem with the internal calibration node in the > Knimesoftware. The node in the OpenMS toppas is working fine because > there the “rscript execution” is already embedded. For the node in the > Knime platform this embedded “rscript execution” is missing and I must > add an input file node with connection to the the calibration node. I > cant find the rscript that is mentioned. > > I hope I write to the correct person to tackle that problem. If note > maybe you can direct me to the right address or forum. > Thanks in advance for your time and hopefully a answers to my > question. > > Best Regards > Simon Redlich > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general -- IPB is hiring: * Researcher (PostDoc Cheminformatics) (m/f/d) https://www.ipb-halle.de/en/career/job-vacancies/joboffer- detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd/ Upcoming events: * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe https://www.nfdi.de/cordi-2023/?lang=en * DGMet September 27th to 29th, 2023, Halle (Saale) https://dgmet.de/event/dgmet-annual-meeting/ * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 --- IPB Halle Computational Plant Biochemistry (CPB) Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Open-ms-general mailing list Ope...@li... https://lists.sourceforge.net/lists/listinfo/open-ms-general _______________________________________________ Open-ms-general mailing list Ope...@li... https://lists.sourceforge.net/lists/listinfo/open-ms-general |
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From: <sim...@un...> - 2023-09-15 12:15:40
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Hallo Steffen, aufgrund deines Namens hoffe ich, dass ich auf deutsch mit dir schreiben kann. Vielen Dank für deine Hilfe. Mein nächstes Anliegen an dich ist eher ein Longshot, da ich nicht weiß, wie gut du dich mit HR-MS auskennen. Ich versuche zur Zeit mithilfe von OpenMS Direct Injectionen in tsv-Dateien umzuwandeln. Mein Work-flow ist im ersten Bild zu sehen. Mein Ziel ist es die centroid Daten (also Signale) unterschiedlichen Messungen in eine tsv Datei zu kombieren. Bevor das aber passieren kann, muss ich zur Zeit händisch jede Messung aufrufen und dort den gewünschten Retentionszeibereich markieren um ein Massenspektrum mehrerer Scans zu erhalten. Dieses Massenspektrum muss dann erneut als raw-Datei exportiert werden. Dazu benötige ich Xcalibur (QualBrowser) von ThermoFisher (wie sie in Bild 2 zu sehen ist). Die neu erstellten raw-Dateien kann dann OpenMS ohne Probleme lesen, zur mzML-Datei umwandeln und in einer tsv-Datei kombinieren. Die Bilder sind in der Powerpoint enthalten Ich würde gerne OpenMS dazu nutzen mir diesen manuellen Teil abzunehmen. Ich denke, dass der SpectraMerger mithilfe der Block_method da weiterhelfen könnte. Leider kommt jedesmal der Fehler: " Error: Unexpected internal error (the given size was not expected: 0)". Leider schaffe ich es nicht diesen Fehler zu beheben. Außerdem wird mir die Fehlermeldung: " TOPPBase.cpp(1634): Error occurred in line 134 of file E:\jenkins\ws\openms\RC\openms_release_packaging\9447518b\source\src\topp\SpectraMerger.cpp (in function: enum OpenMS::TOPPBase::ExitCodes __cdecl TOPPSpectraMerger::main_(int,const char **)) !" ausgegeben wenn ich Debug aktiviere. Vielleicht hilft es ja. Ich kenne mich leider nur geringfügig mit Informatik aus und kann damit wenig anfangen. Falls du eine Möglichkeit kennst das zu beheben oder eine andere Möglichkeit kennst mein Ziel mit openMS zu erreichen, auch gerne mit anderen Nodes, dann würde ich mich sehr freuen und wäre dir sehr dankbar, da dadurch mein Workflow deutlich schlanker werden würde. Dadurch wird meine geplante Publikation übersichtlicher und wäre zu 100% open source. Ich hoffe du verstehst meine Probleme und mein Anliegen. Falls du mir nicht weiterhelfen kannst, möchte ich trotzdem bei dir für die investierte Zeit bedanken. Mit freundlichen Grüßen Simon Redlich -----Original Message----- From: Neumann, Steffen <sne...@ip...> Sent: Donnerstag, 7. September 2023 17:25 To: ope...@li... Subject: Re: [Open-ms-general] Question to Internal Calibration Hi, side-comment: if the path to rscript.exe includes the R version, you'll likely have to change that in case you update R and remove the old version of R, or the Knome node will stop working. Unless you want to install multiple versions of R, you could install it into a path without version. As I don't know Windows and not too much Knime, I can't help with the other problem. Another side comment: instead of the customer support, you are reaching here the developers, power users and generally helpful OpenMS community :-) Grüsse nach Jena, Yours, Steffen On Thu, 2023-09-07 at 13:24 +0200, sim...@un... wrote: > Hello Chris, > thank for your fast respond. > I found the rscript.exe but if I check the File Extension (override)- > box and keep it empty like in your picture KNIME starts to show the > problem “invalid settings: no file extension (override) provided. No > matter what I type in the box as alternative extension its not what > the node wants to have. So, in summary: I could figure out some of my > problems but I’m still stuck and can’t run the node. > > Best regards Simon > > From: Bielow, Chris <Chr...@fu...> > Sent: Mittwoch, 6. September 2023 12:18 > To: General OpenMS discussion <ope...@li...> > Subject: Re: [Open-ms-general] Question to Internal Calibration > > Hi Simon, > > the build-in default value of ‚Rscript‘ does not work in your case > because in general KNIME does not provide the PATH environment to the > nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration > cannot find the ‘Rscript’ executable and you must point to it > manually. > Depending on the system you are on, the location of the ‘Rscript’ > executable will differ. > One easy way to find it, is to use the build-in search functionality > of your operating system, i.e. the Windows Explorer, Nautilus, Finder > etc. > If you are familiar with the commandline, try “where rscript” (for > Windows) or “which Rscript” (for Linux/Mac). This should give you the > desired path, if the R programming language was properly installed on > your system. > If you run KNIME on Windows, you need to check the ‘File Extension > (override)` box, otherwise KNIME will complain that Rscript has an > ‘.exe’ extension – see attached image. > > Hope this helps. > > Cheers > Chris > > > -- > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > www.bsc.fu-berlin.de > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > From: sim...@un... <sim...@un...> > Sent: Tuesday, September 5, 2023 1:16 PM > To: ope...@li... > Subject: [Open-ms-general] Question to Internal Calibration > > Dear customer service, > I have a question regarding the internal calibration node. I > personally prefer to work with OpenMS in the Knime platform. Now I > stumbled over a problem with the internal calibration node in the > Knimesoftware. The node in the OpenMS toppas is working fine because > there the “rscript execution” is already embedded. For the node in > the Knime platform this embedded “rscript execution” is missing and I > must add an input file node with connection to the the calibration > node. I cant find the rscript that is mentioned. > > I hope I write to the correct person to tackle that problem. If note > maybe you can direct me to the right address or forum. > Thanks in advance for your time and hopefully a answers to my > question. > > Best Regards > Simon Redlich > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general -- IPB is hiring: * Researcher (PostDoc Cheminformatics) (m/f/d) https://www.ipb-halle.de/en/career/job-vacancies/joboffer- detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd/ Upcoming events: * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe https://www.nfdi.de/cordi-2023/?lang=en * DGMet September 27th to 29th, 2023, Halle (Saale) https://dgmet.de/event/dgmet-annual-meeting/ * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 --- IPB Halle Computational Plant Biochemistry (CPB) Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 _______________________________________________ Open-ms-general mailing list Ope...@li... https://lists.sourceforge.net/lists/listinfo/open-ms-general |
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From: Neumann, S. <sne...@ip...> - 2023-09-07 19:14:23
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Hi, side-comment: if the path to rscript.exe includes the R version, you'll likely have to change that in case you update R and remove the old version of R, or the Knome node will stop working. Unless you want to install multiple versions of R, you could install it into a path without version. As I don't know Windows and not too much Knime, I can't help with the other problem. Another side comment: instead of the customer support, you are reaching here the developers, power users and generally helpful OpenMS community :-) Grüsse nach Jena, Yours, Steffen On Thu, 2023-09-07 at 13:24 +0200, sim...@un... wrote: > Hello Chris, > thank for your fast respond. > I found the rscript.exe but if I check the File Extension (override)- > box and keep it empty like in your picture KNIME starts to show the > problem “invalid settings: no file extension (override) provided. No > matter what I type in the box as alternative extension its not what > the node wants to have. So, in summary: I could figure out some of my > problems but I’m still stuck and can’t run the node. > > Best regards Simon > > From: Bielow, Chris <Chr...@fu...> > Sent: Mittwoch, 6. September 2023 12:18 > To: General OpenMS discussion <ope...@li...> > Subject: Re: [Open-ms-general] Question to Internal Calibration > > Hi Simon, > > the build-in default value of ‚Rscript‘ does not work in your case > because in general KNIME does not provide the PATH environment to the > nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration > cannot find the ‘Rscript’ executable and you must point to it > manually. > Depending on the system you are on, the location of the ‘Rscript’ > executable will differ. > One easy way to find it, is to use the build-in search functionality > of your operating system, i.e. the Windows Explorer, Nautilus, Finder > etc. > If you are familiar with the commandline, try “where rscript” (for > Windows) or “which Rscript” (for Linux/Mac). This should give you the > desired path, if the R programming language was properly installed on > your system. > If you run KNIME on Windows, you need to check the ‘File Extension > (override)` box, otherwise KNIME will complain that Rscript has an > ‘.exe’ extension – see attached image. > > Hope this helps. > > Cheers > Chris > > > -- > Dr. Chris Bielow > > Bioinformatics Solution Center (BSC) > www.bsc.fu-berlin.de > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room > K21, 14195 Berlin > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > From: sim...@un... <sim...@un...> > Sent: Tuesday, September 5, 2023 1:16 PM > To: ope...@li... > Subject: [Open-ms-general] Question to Internal Calibration > > Dear customer service, > I have a question regarding the internal calibration node. I > personally prefer to work with OpenMS in the Knime platform. Now I > stumbled over a problem with the internal calibration node in the > Knimesoftware. The node in the OpenMS toppas is working fine because > there the “rscript execution” is already embedded. For the node in > the Knime platform this embedded “rscript execution” is missing and I > must add an input file node with connection to the the calibration > node. I cant find the rscript that is mentioned. > > I hope I write to the correct person to tackle that problem. If note > maybe you can direct me to the right address or forum. > Thanks in advance for your time and hopefully a answers to my > question. > > Best Regards > Simon Redlich > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general -- IPB is hiring: * Researcher (PostDoc Cheminformatics) (m/f/d) https://www.ipb-halle.de/en/career/job-vacancies/joboffer- detail/wissenschaftliche-r-mitarbeiter-in-postdoc-chemieinformatik-mwd/ Upcoming events: * CoRDI 2023, 12.-14.09.2023 @ Karlsruhe https://www.nfdi.de/cordi-2023/?lang=en * DGMet September 27th to 29th, 2023, Halle (Saale) https://dgmet.de/event/dgmet-annual-meeting/ * 2nd ELIXIR-DE Hackathon, 11-15 December 2023 in Bielefeld https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2 --- IPB Halle Computational Plant Biochemistry (CPB) Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 Tel. +49 (0) 345 5582 - 1470 06120 Halle +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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From: <sim...@un...> - 2023-09-07 12:03:34
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Hello Chris, thank for your fast respond. I found the rscript.exe but if I check the File Extension (override)-box and keep it empty like in your picture KNIME starts to show the problem invalid settings: no file extension (override) provided. No matter what I type in the box as alternative extension its not what the node wants to have. So, in summary: I could figure out some of my problems but Im still stuck and cant run the node. Best regards Simon From: Bielow, Chris <Chr...@fu...> Sent: Mittwoch, 6. September 2023 12:18 To: General OpenMS discussion <ope...@li...> Subject: Re: [Open-ms-general] Question to Internal Calibration Hi Simon, the build-in default value of Rscript does not work in your case because in general KNIME does not provide the PATH environment to the nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration cannot find the Rscript executable and you must point to it manually. Depending on the system you are on, the location of the Rscript executable will differ. One easy way to find it, is to use the build-in search functionality of your operating system, i.e. the Windows Explorer, Nautilus, Finder etc. If you are familiar with the commandline, try where rscript (for Windows) or which Rscript (for Linux/Mac). This should give you the desired path, if the R programming language was properly installed on your system. If you run KNIME on Windows, you need to check the File Extension (override)` box, otherwise KNIME will complain that Rscript has an .exe extension see attached image. Hope this helps. Cheers Chris -- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de <http://www.bsc.fu-berlin.de> Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de From: sim...@un... <mailto:sim...@un...> <sim...@un... <mailto:sim...@un...> > Sent: Tuesday, September 5, 2023 1:16 PM To: ope...@li... <mailto:ope...@li...> Subject: [Open-ms-general] Question to Internal Calibration Dear customer service, I have a question regarding the internal calibration node. I personally prefer to work with OpenMS in the Knime platform. Now I stumbled over a problem with the internal calibration node in the Knimesoftware. The node in the OpenMS toppas is working fine because there the rscript execution is already embedded. For the node in the Knime platform this embedded rscript execution is missing and I must add an input file node with connection to the the calibration node. I cant find the rscript that is mentioned. I hope I write to the correct person to tackle that problem. If note maybe you can direct me to the right address or forum. Thanks in advance for your time and hopefully a answers to my question. Best Regards Simon Redlich |
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From: Bielow, C. <Chr...@fu...> - 2023-09-06 10:33:51
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Hi Simon, the build-in default value of Rscript does not work in your case because in general KNIME does not provide the PATH environment to the nodes it invokes (as opposed to TOPPAS). Thus, InternalCalibration cannot find the Rscript executable and you must point to it manually. Depending on the system you are on, the location of the Rscript executable will differ. One easy way to find it, is to use the build-in search functionality of your operating system, i.e. the Windows Explorer, Nautilus, Finder etc. If you are familiar with the commandline, try where rscript (for Windows) or which Rscript (for Linux/Mac). This should give you the desired path, if the R programming language was properly installed on your system. If you run KNIME on Windows, you need to check the File Extension (override)` box, otherwise KNIME will complain that Rscript has an .exe extension see attached image. Hope this helps. Cheers Chris -- Dr. Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de From: sim...@un... <sim...@un...> Sent: Tuesday, September 5, 2023 1:16 PM To: ope...@li... Subject: [Open-ms-general] Question to Internal Calibration Dear customer service, I have a question regarding the internal calibration node. I personally prefer to work with OpenMS in the Knime platform. Now I stumbled over a problem with the internal calibration node in the Knimesoftware. The node in the OpenMS toppas is working fine because there the rscript execution is already embedded. For the node in the Knime platform this embedded rscript execution is missing and I must add an input file node with connection to the the calibration node. I cant find the rscript that is mentioned. I hope I write to the correct person to tackle that problem. If note maybe you can direct me to the right address or forum. Thanks in advance for your time and hopefully a answers to my question. Best Regards Simon Redlich |
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From: <sim...@un...> - 2023-09-05 11:35:59
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Dear customer service, I have a question regarding the internal calibration node. I personally prefer to work with OpenMS in the Knime platform. Now I stumbled over a problem with the internal calibration node in the Knimesoftware. The node in the OpenMS toppas is working fine because there the "rscript execution" is already embedded. For the node in the Knime platform this embedded "rscript execution" is missing and I must add an input file node with connection to the the calibration node. I cant find the rscript that is mentioned. I hope I write to the correct person to tackle that problem. If note maybe you can direct me to the right address or forum. Thanks in advance for your time and hopefully a answers to my question. Best Regards Simon Redlich |
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From: Bielow, C. <Chr...@fu...> - 2023-08-01 09:47:15
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Thanks to everyone who shared their thoughts! We received plenty of replies already. The survey will close in three days, so if you want to share some last-minute input, please do so at <https://www.surveymonkey.de/r/9F6TMJL> https://www.surveymonkey.de/r/9F6TMJL Thanks again! The OpenMS team From: Bielow, Chris Sent: Monday, July 24, 2023 10:17 AM To: ope...@li...; ope...@li... Subject: OpenMS user survey Folks! We have created a survey to better understand users' experience with OpenMS. The survey is short, and we would love to hear your opinions on what's good and bad! Please share your thoughts on https://www.surveymonkey.de/r/9F6TMJL Thanks in advance and have a great week! The OpenMS team |
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From: Annie B. S. <as...@se...> - 2023-07-25 20:32:26
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unsubscribe Wishing you all the best, *Annie B. Sanger* Senior International Account Manager Sepax Technologies, Inc. 5 Innovation Way Newark, DE, 19711, USA Cell Phone: 1-747-227-4752 Main Phone: (302) 366-1101 Skype: live:asanger_3 Email: as...@se... www.linkedin.com/in/anniebsays www.sepax-tech.com On Tue, Jul 25, 2023 at 12:29 PM Bielow, Chris <Chr...@fu...> wrote: > Dear all, > > > > we are proud to announce the major release of OpenMS 3.0.0 (June 2023). > > > > Please find all the details, including a Changelog and Installation > Instructions here: > > > > https://github.com/OpenMS/OpenMS/releases/tag/Release3.0.0 > > > > Please feel free to connect with us on Discord ( > https://discord.gg/4TAGhqJ7s5) and chat with us about the release or > OpenMS in general. > > > > Yours truly, > > The OpenMS team > > > > > > -- > > Chris Bielow > > > > Bioinformatics Solution Center (BSC) > > www.bsc.fu-berlin.de > > Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, > 14195 Berlin > > Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de > > > _______________________________________________ > Open-ms-general mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open-ms-general > -- ****************************** This email message from Sepax Technologies, Inc. is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. |
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From: Bielow, C. <Chr...@fu...> - 2023-07-25 19:29:03
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Dear all, we are proud to announce the major release of OpenMS 3.0.0 (June 2023). Please find all the details, including a Changelog and Installation Instructions here: https://github.com/OpenMS/OpenMS/releases/tag/Release3.0.0 Please feel free to connect with us on Discord (https://discord.gg/4TAGhqJ7s5) and chat with us about the release or OpenMS in general. Yours truly, The OpenMS team -- Chris Bielow Bioinformatics Solution Center (BSC) www.bsc.fu-berlin.de Freie Universität Berlin, Institut für Informatik, Takustr. 9, room K21, 14195 Berlin Phone: +49 (0)30 838-63084, Email: Chris.Bielow(at)bsc.fu-berlin.de |
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From: Bielow, C. <Chr...@fu...> - 2023-07-24 08:32:53
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Folks! We have created a survey to better understand users' experience with OpenMS. The survey is short, and we would love to hear your opinions on what's good and bad! Please share your thoughts on https://www.surveymonkey.de/r/9F6TMJL Thanks in advance and have a great week! The OpenMS team |
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