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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: Bielow, C. <Chr...@fu...> - 2023-08-01 09:47:14
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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: 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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From: Timo S. <sac...@gm...> - 2020-10-03 12:46:36
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Dear OpenMS-Users, we are proud to announce the release of OpenMS 2.6.0. Grab our binary installers here <https://abibuilder.informatik.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/2.6.0> Our bioconda packages are available here <https://anaconda.org/search?q=OpenMS> KNIME plugins are available soon via the KNIME update mechanism. And our pyOpenMS 2.6.0 packages will be available soon here <https://pypi.org/project/pyopenms/> In the following you find all important changes to the previous version: We now create nightly pyopenms wheels ( https://pypi.org/project/pyopenms-nightly/) and conda packages ( https://anaconda.org/OpenMS/) Adapters/Third-party support: - LuciphorAdapter now stores which modifications were used for localization (#4771 <https://github.com/OpenMS/OpenMS/pull/4771>) and localization scores are reported in mzTab #4772 <https://github.com/OpenMS/OpenMS/pull/4772> - Added Percolator3.0 support, fixed ConsensusID reading from wrong (Percolator-overwritten) meta data (#4829 <https://github.com/OpenMS/OpenMS/pull/4829>), and adapted the Regex parsing of XTandem Percolator output files #4849 <https://github.com/OpenMS/OpenMS/pull/4849> - Added options introduced in new MSGF versions #4713 <https://github.com/OpenMS/OpenMS/pull/4713> - Updated IsoSpec fine structure isotopic calculator sources to v 2.1.0 #4733 <https://github.com/OpenMS/OpenMS/pull/4733> - Updated other third-party tools What's new: - Introduced a Wizard for Swath data (#4647 <https://github.com/OpenMS/OpenMS/pull/4647> #4706 <https://github.com/OpenMS/OpenMS/pull/4706> #4758 <https://github.com/OpenMS/OpenMS/pull/4758> #4769 <https://github.com/OpenMS/OpenMS/pull/4769> #4773 <https://github.com/OpenMS/OpenMS/pull/4773> #4837 <https://github.com/OpenMS/OpenMS/pull/4837>), which also reports summary statistics about Swath TargetedExperiments #4788 <https://github.com/OpenMS/OpenMS/pull/4788> #4790 <https://github.com/OpenMS/OpenMS/pull/4790> - UTIL StaticModification: Applies a set of modifications to all PeptideIDs in an idXML file (UTIL) - TOPP DatabaseSuitability: Computes a suitability score for a database which was used for a peptide identification search. Also reports the quality of LC-MS spectra. #4791 <https://github.com/OpenMS/OpenMS/pull/4791> #4781 <https://github.com/OpenMS/OpenMS/pull/4781> #4814 <https://github.com/OpenMS/OpenMS/pull/4814> - Added support for QC of labeled experiments (iTRAQ/TMT) - Added automated QC computations for MRM (#4637 <https://github.com/OpenMS/OpenMS/pull/4637>) - Adapted consensusXML and mzTab to support protein groups (#4630 <https://github.com/OpenMS/OpenMS/pull/4630>) - Consensus/IDMerger: Introduced use of merge idx to ensure keeping track of primaryRuns - Epifany: Added calculation of protein group FDR, ID filtering for protein group scores (#4802 <https://github.com/OpenMS/OpenMS/pull/4802>) and support for inference on not just individual samples but also consensusXML files - FeatureFinderCentroided/FeatureFinderAlgorithmPicked: Improved runtime performance #4652 <https://github.com/OpenMS/OpenMS/pull/4652> #4701 <https://github.com/OpenMS/OpenMS/pull/4701> - FeatureFinderIdentification: Improved SLIM-labeling experiment support - FileConverter: Improved runtime performance when producing mzML output #4750 <https://github.com/OpenMS/OpenMS/pull/4750> - FeatureLinkerQT: Introduced Fibonacci heaps for large runtime optimization (#4721 <https://github.com/OpenMS/OpenMS/pull/4721>) and fixed related preconditions/segfaults #4756 <https://github.com/OpenMS/OpenMS/pull/4756> #4760 <https://github.com/OpenMS/OpenMS/pull/4760> #4778 <https://github.com/OpenMS/OpenMS/pull/4778> - IDFilter: added support for consensusXMLs #4798 <https://github.com/OpenMS/OpenMS/pull/4798> #4799 <https://github.com/OpenMS/OpenMS/pull/4799> - MapAlignerIdentification: New option to use an "identity" transformation when data is too sparse to determine alignment model #4628 <https://github.com/OpenMS/OpenMS/pull/4628> - MzTabExporter: changed to only export one main score, and to derive nativeIDs from data (#4767 <https://github.com/OpenMS/OpenMS/pull/4767>). Now ensures that all output rows contain the same number of columns #4801 <https://github.com/OpenMS/OpenMS/pull/4801> - MzTabExporter on LFQ consensusXMLs produces 100% PRIDE validated mzTabs now - ProteomicsLFQ: Added spectral counting as quantification method (#4726 <https://github.com/OpenMS/OpenMS/pull/4726>). Introduced performance improvements for AASequence and string parsing, especially for modified sequences. Various further improvements (e.g. #4669 <https://github.com/OpenMS/OpenMS/pull/4669>) - SimpleSearchEngine (multithreaded), TheoreticalSpectrumGenerator, MSSpectrum: Runtime optimization #4709 <https://github.com/OpenMS/OpenMS/pull/4709> - Further introduction of more file streaming to address possible memory consumption issues #4682 <https://github.com/OpenMS/OpenMS/pull/4682> #4694 <https://github.com/OpenMS/OpenMS/pull/4694> Further fixes: - We now limit double precision to 17 digits during file writes #4636 <https://github.com/OpenMS/OpenMS/pull/4636> - Ensure that CometAdapter always writes indexed mzML fixes for CometAdapter (#4653 <https://github.com/OpenMS/OpenMS/pull/4653>), fixed the writing of terminal modifications with specific origin in Comet ( #4742 <https://github.com/OpenMS/OpenMS/pull/4742>), the writing of protein terminal mods in Comet and MSGF adapter #4710 <https://github.com/OpenMS/OpenMS/pull/4710>, and the Comet pepXML modification parsing #4755 <https://github.com/OpenMS/OpenMS/pull/4755> - Removed secondary search engine settings duplication in mzTab MTD section. #4720 <https://github.com/OpenMS/OpenMS/pull/4720> - Improved XTandem output protein parsing #4789 <https://github.com/OpenMS/OpenMS/pull/4789> to fix Issue #4770 <https://github.com/OpenMS/OpenMS/issues/4770> - Increased (partial) support for parsing mzid with nonstandard, non-CV-term scores, fixes #4859 <https://github.com/OpenMS/OpenMS/pull/4859> - Fixes to NucleicAcidSearchEngine mzTab output #4692 <https://github.com/OpenMS/OpenMS/pull/4692> - ConsensusID now passes spectrum reference meta values along #4703 <https://github.com/OpenMS/OpenMS/pull/4703> - Fix to LFQ requantification #4633 <https://github.com/OpenMS/OpenMS/pull/4633> - Improved MapAlignerTreeGuided memory usage (#4704 <https://github.com/OpenMS/OpenMS/pull/4704>) and fixed segfault when featureXML contains no IDs #4665 <https://github.com/OpenMS/OpenMS/pull/4665> - TOPPAS fixes #4780 <https://github.com/OpenMS/OpenMS/pull/4780> Various: - OMMSAAdapter now writes out native ids and spectrum references #4852 <https://github.com/OpenMS/OpenMS/pull/4852> - FileInfo: Report more charge distribution and MS2 activation-method information for Raw files #4836 <https://github.com/OpenMS/OpenMS/pull/4836> - Added sum formula output in RNAMassCalculator #4677 <https://github.com/OpenMS/OpenMS/pull/4677> - Added automatic OpenMS tool reporting of peak memory usage #4712 <https://github.com/OpenMS/OpenMS/pull/4712> - Some extra tools documentation outputs #4822 <https://github.com/OpenMS/OpenMS/pull/4822> #4823 <https://github.com/OpenMS/OpenMS/pull/4823> - Extended mapping of filetypes and mimetypes for knime output formats documentation #4839 <https://github.com/OpenMS/OpenMS/pull/4839> - RTEvaluation: fixed output formats #4533 <https://github.com/OpenMS/OpenMS/pull/4533> - Some further clarifications, standardization/consolidation of outputs formats/consistency - Continued fixes/improvement of documentation - Removed deprecated version of PeakPickerHiRes (LowMemPeakPickerHiResRandomAccess and LowMemPeakPickerHiRes). Their functionality can be accessed through options of PeakPickerHiRes Enjoy, The OpenMS-Developers |
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From: Timo S. <sac...@in...> - 2020-06-17 08:34:10
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Dear OpenMS users, As part of CIBI/de.NBI training network we now offer an online meeting to provide first hand support. Think of it as a web-based video help desk for proteomics and metabolomics researchers and associated bioinformaticians and data analysts that use or consider using OpenMS. You find details and a link to register to our "Data and Code clinic" here: https://www.denbi.de/training/917-cibi-data-clinic-june-2020 Best, The OpenMS team -- Dr. Timo Sachsenberg PostDoc, Applied Bioinformatics Group Eberhard Karls Universität Tübingen Phone: +49 7071 29 70461 E-Mail: sac...@in... Currently working from home |
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From: Timo S. <sac...@gm...> - 2020-06-04 10:11:16
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Dear fellow (and future) OpenMS developers, you might know that our last developer meeting got canceled because of the COVID situation. We will have a free virtual developer meeting in the week 3-7 August so please mark that date in your calendar. Details will follow. Best, Timo |
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From: Timo S. <sac...@gm...> - 2020-01-27 15:56:06
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Dear fellow (and future) OpenMS developers, We would kindly invite you to register for the OpenMS developer meeting. You are cordially invited to the 2020 OpenMS Developer's Retreat, which will take place 15-21 March 2020 near Corinth in Greece. Please forward this invitation to interested parties. As in previous years, places are limited as we will stay in a villa. However, we still have a couple of places available for anyone interested in developing tools and algorithms in and around OpenMS. We discuss further directions of OpenMS and give developers the possibility to briefly report on their implementations. We also provide training for novel developers. There will most likely be a social event (e.g., visiting Corinth on an afternoon and having dinner) and in general, it's a very relaxed setting with lots of coding/hackathons/building workflows. Please register to secure your stay at https://docs.google.com/forms/d/e/1FAIpQLSdHk9PG1GDOBNfAqVidWoAy_ndPgq4PPRGUoA4HghWp8rzTcQ/viewform?vc=0&c=0&w=1 and provide expected arrival/departure day to easy travel arrangements. The house is booked from March 15th in the afternoon until March 21st in the morning, and we anticipate that most people will arrive on March 15th and depart on March 21th. The estimated cost of the stay will be approx. 500 € per person and the whole week (we share food and rent). There is room for everyone (though you might need to share a room), WIFI is available and we are going to divide costs for food and the stay (which is relatively cheap compared to a hotel). Best, The OpenMS team |
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From: Timo S. <sac...@gm...> - 2019-03-04 13:40:32
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Dear fellow (and future) OpenMS developers, We would kindly invite you to register for the OpenMS developer meeting. Slots are filling up quickly so don't wait too long. It will take place from 7-13 April 2019 in Belgrad, Serbia. As in previous years, places are limited as we will stay in a villa. We discuss further directions of OpenMS and give developers the possibility to briefly report on their implementations. We also provide training for novel developers. There will most likely be a social event (e.g., visiting the city center on an afternoon and having dinner) and in general, it's a very relaxed setting with lots of coding/hackathons/building workflows. Please register to secure your stay at https://goo.gl/forms/fntq7Rj7bsUaKJ4P2 and provide expected arrival/departure day to easy travel arrangements. The estimated cost of the stay will be approx. 500 € per person and the whole week (we share food and rent). We anticipate that most people will arrive on April 7th and depart on April 12th or April 13th. There is room for everyone (though you might need to share a room), WIFI and we are going to divide costs for food and the stay (which is comparably cheap compared with a hotel). Best, The OpenMS team |
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From: Timo S. <sac...@gm...> - 2019-02-05 10:40:12
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Dear fellow (and future) OpenMS developers, We would kindly invite you to register for the OpenMS developer meeting. It will take place from 7-13 April 2019 in Belgrad, Serbia. As in previous years, places are limited as we will stay in a villa. We discuss further directions of OpenMS and give developers the possibility to briefly report on their implementations. We also provide training for novel developers. There will most likely be a social event (e.g., visiting the city center on an afternoon and having dinner) and in general, it's a very relaxed setting with lots of coding/hackathons/building workflows. Please register to secure your stay at https://goo.gl/forms/fntq7Rj7bsUaKJ4P2 and provide expected arrival/departure day to easy travel arrangements. The estimated cost of the stay will be approx. 500 € per person and the whole week (we share food and rent). We anticipate that most people will arrive on April 7th and depart on April 12th or April 13th. There is room for everyone (though you might need to share a room), WIFI and we are going to divide costs for food and the stay (which is comparably cheap compared with a hotel). Best, The OpenMS team |
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From: Julian U. <jul...@ru...> - 2018-09-25 11:33:49
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Dear colleague, dear member of the proteomics community, The deadline for registration is approaching, but we still have some free places for the "*Tool Training for Proteomics*" which will be hosted on 16th October 2018 at Ruhr University Bochum as part of the de.NBI (www.denbi.de) training programme and is completely free of charge for all attendees. The course is directed at everyone who works with MS proteomics data, beginner and advanced levels. You do not need to have a deep level of computational knowledge, but should know the basics of MS proteomics data analysis. Besides the tool based sessions we offer a "bring your own data" session to discuss and try out analysis strategies of your own special data. The number of participants is limited, please register soon at https://goo.gl/2ctFNe Further information about the course is available at the registration page and at http://www.denbi.de/22-training-cat/training-courses/606-tool-training-for-proteomics If you have any questions don’t hesitate to contact us via bio...@ru... Please also forward this message to potentially interested colleagues. Best regards, Julian Uszkoreit (on behalf of BioInfra.Prot, a service unit of de.NBI) |
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From: Julian U. <jul...@ru...> - 2018-09-10 08:14:53
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Dear colleague, dear member of the proteomics community, we would like to call your attention to the training course "*Tool Training for Proteomics*" which will be hosted on 16th October 2018 at Ruhr University Bochum as part of the de.NBI (www.denbi.de) training programme and is completely free of charge for all attendees. The course is directed at everyone who works with MS proteomics data, beginner and advanced levels. You do not need to have a deep level of computational knowledge, but should know the basics of MS proteomics data analysis. Besides the tool based sessions we offer a "bring your own data" session to discuss and try out analysis strategies of your own special data. As the number of participants is limited, please register soon at https://goo.gl/2ctFNe Further information about the course is available at the registration page and at http://www.denbi.de/22-training-cat/training-courses/606-tool-training-for-proteomics If you have any questions don’t hesitate to contact us via bio...@ru... Please also forward this message to potentially interested colleagues. Best regards, Julian Uszkoreit (on behalf of BioInfra.Prot, a service unit of de.NBI) -- Dr. rer. nat. JULIAN USZKOREIT PostDoc Ruhr-Universität Bochum Medizinisches Proteom-Center DEPARTMENTS Medical Bioinformatics / Functional Proteomics Building ZKF 1.054 | Universitätsstr. 150 | D-44801 Bochum Fon +49 (0)234 32 29283 | Fax +49 (0)234 32 14554 E-Mail jul...@ru... |
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From: Timo S. <sac...@gm...> - 2018-08-14 10:20:51
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*Joint CIBI/OpenMS user meeting* Dear friends and colleagues, we are happy to announce the 2nd CIBI User Meeting on 19. September (09:00) until 21. September 2018 (16:00) at Freie Universität Berlin, Steintor-Campus, Arnimallee 6, 14195 Berlin, Germany *OpenMS, MetFrag, FIJI, and SeqAn are developed by members of the Center for Integrative Bioinformatics (CIBI) and partially funded as a project of the German** network for bioinformatic infrastructure (de.NBI). Since 2017 the OpenMS user **meeting is part of the larger CIBI user meeting. Participants have the opportunity to select which tracks they want to attend. This year, we also offer a dedicated track for users that want to develop computational tools.* During the meeting, we will present the capabilities of CIBI tools OpenMS, MetFrag, FIJI, and SeqAn, and discuss your needs and future directions in mass spectrometry and sequence analysis. This year’s meeting will include an* optional OpenMS tutorial session on the first day (Wednesday, September 19)* with the *general conference starting on Thursday, September 20*. Traditionally, the schedule of our meetings is very flexible, allowing discussions and contributions from the participants. You can *bring your data*, a *wish list*, *ideas for collaboration projects*, and also *give a talk about your project*. This may include suggestions in areas where currently available software solutions were unsatisfactory. You will find detailed information on our registration page: https://sites.google.com/view/cibi-user-meeting-2018/home (registration opens soon) See you in Berlin! The CIBi Team |
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From: Timo S. <sac...@gm...> - 2018-01-08 14:21:33
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Dear OpenMS users, *We are proud to announce the new OpenMS release (version 2.3.0). * Binary packages for Windows (64-bit) and Mac OS X dmg (64-bit) are available at: https://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS -2.3/ PyOpenMS and docker images will follow shortly. Notable changes since release version 2.2 (source-only) are: *New tools:* - CometAdapter -- Annotates MS/MS spectra using Comet (TOPP) - MetaboliteAdductDecharger -- Decharges and merges different feature charge variants of the same metabolite (UTIL) - OpenPepXL -- Tool for protein-protein cross-linking identification using labeled linkers (UTIL) - OpenPepXLLF -- Tool for protein-protein cross-linking with label-free linkers (UTIL) - PSMFeatureExtractor -- Computes extra features for each input PSM (UTIL) - SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry (UTIL) - XFDR -- Calculates false discovery rate estimates on protein-protein-crosslink identifications (UTIL) *Major changes in functionality:* - Experimental design - Add support for fractions (experimental) - FeatureLinkerUnlabeledKD - m/z and retention time tolerances for warping and linking are now separate parameters - IsobaricAnalyzer - Support for TMT11plex ( https://www.thermofisher.com/order/catalog/product/A34808) - FileInfo - For idXML files, the tool computes the average length of contained peptides - TopPerc - Renamed in PercolatorAdapter (still experimental) *TOPPView:* - Deletion of selections of Peak Annotations is reflected in the Peptide Hit - Buttons for saving ID files were merged to one single button. Format is determined by file extension or selected filter - Clicking on a data point in 2D view, the search range for close fragment ion spectra is extended if no spectra are found initially *Renamed tool:* - LowMemPeakPickerHiRes_RandomAccess was renamed to LowMemPeakPickerHiResRandomAccess *OpenSWATH:* - RT normalization now allows more models - Add S/N ratio for each ion trace *Library:* - TOPP tools report their peak memory usage when using -debug 1 (or higher) - idXML files can now be written faster (about 10%) - pyOpenMS bindings for DataArrayByName getters - Python build is now split into compilation units and can thus run in parallel - FASTA files can now be written - Allow String values to be passed to EnzymaticDigestion::isValidProduct *File formats:* - consensusXML now supports both channels and MS runs. Information will also be exported in mzTab *Third-party software:* - New: Comet "2016.01 rev. 3" for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit - New: Percolator 3.1.2 for Windows 32bit/64bit, Linux 64bit, and MacOS 64bit (still experimental) - New: Sirius 3.5.1 for Windows 64bit, Linux 64bit, and MacOS 64bit - New: SpectraST 5.0 for Windows 64bit, Linux 64bit, and MacOS 64bit - Update MS-GF+ to Release (v2017.07.21) Have fun, The OpenMS-Developers |
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From: Julian U. <jul...@ru...> - 2017-10-17 18:39:49
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Dear colleague, dear member of the proteomics community, we would like to call your attention to the training course "Tool Training for Proteomics“ which we will be hosted on 7th December 2017 at Ruhr-University Bochum as part of de.NBI (www.denbi.de). As the number of participants is limited, please register soon at https://goo.gl/sd7bMc if you are interested. Further information about the course is also available at http://www.denbi.de/22-training-cat/training-courses/418-ttp If you have any questions don’t hesitate to contact us via bio...@ru... Please also forward this message to potentially interested colleagues. Best regards, Julian Uszkoreit -- Dr. rer. nat. JULIAN USZKOREIT PostDoc Ruhr-Universität Bochum Medizinisches Proteom-Center DEPARTMENTS Medical Bioinformatics / Functional Proteomics Building ZKF 1.054 | Universitätsstr. 150 | D-44801 Bochum Fon +49 (0)234 32 29275 | Fax +49 (0)234 32 14554 E-Mail jul...@ru... |
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From: Timo S. <sac...@in...> - 2017-07-20 10:46:39
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Joint CIBI user meeting featuring: OpenMS + MetFrag: High-performance software for high-throughput proteomics and metabolomics and SeqAn: C++ library of efficient algorithms and data structures for the analysis of biological sequence data. Dear friends and colleagues, we are happy to announce the 10th CIBI User Meeting on 25. September (09:00) until 27. September 2017 (16:00) at Martin-Luther University, Steintor-Campus, Room SR7, Emil-Abderhalden-Straße, 06108 Halle, Germany Note: OpenMS, MetFrag, and SeqAn are developed by the Center for Integrative Bioinformatics (CIBI) and funded as a project of the german network for bioinformatic infrastructure (de.NBI). Thus, for the first time, the OpenMS user meeting is part of a larger CIBI user meeting. Participants may select if they want to participate in the OpenMS or SeqAn track. We also offer a dedicated track for users that want to develop computational tools with OpenMS and SeqAn as well as an introduction to MetFrag. During the meeting, we will present the capabilities of CIBI tools OpenMS, MetFrag and SeqAn, and discuss your needs and future directions in mass spectrometry and sequence analysis. This year’s meeting will include an optional OpenMS tutorial session on the first day (Monday, September 25) with the general conference starting on Tuesday, September 26. Traditionally, the schedule of our meetings is very flexible, allowing discussions and contributions from the participants. You can bring your data, a wish list, ideas for collaboration projects, and also give a talk about your project. This may include suggestions in areas where currently available software solutions were unsatisfactory. We would be very happy to welcome you in Halle this year. Accommodation Please take care of room reservations yourself. We can suggest the following options. Prices etc. are only indicative and not guaranteed. Hotel Am Steintor (close to Workshop location)https://www.am-steintor.de <https://www.am-steintor.de/>40 EUR single room, 55 EUR double roomHostel No5 (20 min walk, or Tram connection, Nr 2 and Nr 5)http://www.hostel-no5.de/hostel_lage1.htmlsingle room: 25 EUR per night | double room: 40 EUR per night | triple room: 15 EUR per night and personstudio (single room, separate bath, kitchen): 40 EUR per night (single) or 50 EUR per night (double)plus breakfast: 4 EUR per day and person (must be ordered before arrival)Hotel Ankerhof (20 min walk or direct Tram connection, Nr 2 and Nr 5)http://www.leipziggrafik.de/anker05/htdocs/anfahrt.shtmlspecial rate (incl. breakfast) is 65 EUR per person and night with booking code: «Leibniz Institut für Pflanzenbiochemie»Further accommodation options:http://www.hrs.de <http://www.hrs.de/>https://www.couchsurfing.org/ Journey Directions to the Steintor Campus Uni Halle: https://goo.gl/ZNSmBM By train: Halle is well connected within Germany’s network of IC and ICE trains https://reiseauskunft.bahn.de/bin/query2.exe/en By plane: Nearest airports are Halle-Leipzig (LEJ), Erfurt (ERF), Berlin (TXL & SXF). Shortest connection is via Halle-Leipzig Airport, but flights might not run every day. Nice connections are possible via Berlin with train to Halle (Saale) and via Frankfurt (FRA) using the ICE train connection. Note that the Berlin airport BER is still not opened. Public transport in Halle: https://goo.gl/9Zo5vy, http://www.havag.com/fahrplan/liniennetz-und-tarifzonenplan Registration Participants need to register via https://goo.gl/forms/8WKW2T2OBrosfiuA3. The deadline for the workshop registration is 31. July 2017. Notification of acceptance is 15. August 2017. The workshop fee is 50 € for students (Undergrad / PhD), and 80 € for Industry, PostDoc, PI, Professor or above. Fees will cover coffee breaks, lunch, and the workshop dinner. Schedule TBA Speaker: We are excited to have Keynote talks by Wolfram Weckwerth (MOSYS, Uni Vienna), Greg Landrum (RDKIT/KNIME), Ivo Grosse (MLU Halle), and Steffen Neumann (IPB Halle) Contact sac...@in... – scientific and program questions See you in Halle! The CIBi Team |
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From: Timo S. <sac...@gm...> - 2017-07-03 07:53:48
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OpenMS 2.2 is a source-only release. It introduces a considerable number of new features and bug fixes. We recommend checking out the *Release2.2.0 *git tag ( https://github.com/OpenMS/OpenMS/releases/tag/Release2.2.0). Alternatively, you can download the full source code at https://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.2. *Notable changes since version 2.1 are:* *Databases:* - By default, decoy sequences are now denoted by the prefix "DECOY_" *New tools:* - FeatureLinkerUnlabeledKD -- Fast feature linking using a KD tree (TOPP) - SpectraSTSearchAdapter -- Interface to the SEARCH Mode of the SpectraST executable (UTIL) - DatabaseFilter -- Filters a protein database (FASTA format) based on identified proteins (UTIL) - TargetedFileConverter -- Conversion of multiple targeted file formats (CSV, TraML, etc.) - RNPxlSearch -- Annotate RNA to peptide crosslinks in MS/MS spectra (UTIL) *Deprecated and removed tools:* - ITRAQAnalyzer -- superseded by IsobaricAnalyzer - TMTAnalyzer -- superseded by IsobaricAnalyzer - ConvertTSVToTraML - superseded by TargetedFileConverter - ConvertTraMLToTSV - superseded by TargetedFileConverter - MapAlignmentEvaluation -- removed as deprecated *Major changes in functionality:* - OpenSWATH analysis - Support for metabolomics workflows - Support for scanning SWATH (SONAR) - Support for SQL-based file formats - XTandemAdapter - Simplified usage - Improved support for PTMs and newer X! Tandem versions ("Vengeance", "Alanine") - IsobaricAnalyzer - Support for TMT10plex - Support for quantification in MS3 data - IDMapper - Allows to map unidentified tandem mass spectra to features - FeatureFinderIdentification - Advanced multi-sample support using machine learning - FileFilter - Allows users to enable zlib and lossy compression (see "-lossy_compression") - Allows users to set desired mass accuracy - IDFilter - Added option to filter for valid digestion products - FalseDiscoveryRate - Allow filtering by q-value in the tool (no need for IDFilter with "score:pep" option) *Library:* - Averagine approximation for fragment isotope distributions - Precursor mass correction supports correction to highest intensity peak in tolerance window - Functionality for resampling and adding of spectra - Protein-protein cross-link spectrum generator - Terminal modifications are now separated by "." in text output - SQLite support in OpenSWATH - TheoreticalSpectrumGenerator speed-up and removal of RichPeak code - Removal of template parameters from MSExperiment (reduced compile time and binary size) - Allow estimation of isotope distributions with predefined numbers of sulfur atoms - Improved handling of bracket notation for modified residues (e.g. N[2457.877]VSVK) - Improved handling of terminal and residue specificity of modifications - Improved annotation of peptide identifications with spectrum references - Improved handling of unknown amino acids ("X") in sequences *File formats:* - Improved mzML support for SONAR data and mzML with drift time (experimental) - Improved support for cross-link data and unknown modifications in mzIdentML - mzXML writer able to write MaxQuant-compatible files - mzML files now routinely support substantial compression (up to 5x compression, see #2449 <https://github.com/OpenMS/OpenMS/pull/2449>, #2458 <https://github.com/OpenMS/OpenMS/pull/2458>) - Support for Percolator result files based on X! Tandem searches *Scripts:* - New R script for visualizing RT transformations (trafoXML) *Known Build Issues:* You might encounter build issues on recent compilers. We recommend using Visual Studio Version 2015 and GCC 5.0 or older. The OpenMS Developers |
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From: Timo S. <sac...@gm...> - 2016-11-22 12:36:51
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We are proud to announce the new OpenMS release (version 2.1). Binary packages for Windows (64-bit) and Mac OS X dmg (64-bit):* OpenMS binary release 2.1.0 <https://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.1/>* The online documentation contains the installation instructions <http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/index.html> . *To use OpenMS in KNIME, please follow the instruction on: *OpenMS 2.1 installation in KNIME <https://www.openms.de/download/knime-plugin/> *Notable changes since version 2.0.1 are:* *New tools:* - ExternalCalibration — Applies an external mass recalibration - OpenSwathFileSplitter — Splits SWATH files into n files, each containing one window - MultiplexResolver — Completes peptide multiplets and resolves conflicts within them - TICCalculator — Calculates the TIC from a mass spectrometric raw file (useful for benchmarking) *Deprecated and removed tools:* - PILISIdentification — performs a peptide/protein identification with the PILIS engine - PILISModelCV — Perform a cross-validation of the PILIS model parameters - PILISModelTrainer — Train the PILIS model with a given set of spectra and identifications - PILISSpectraGenerator — Generate spectra, given a list of peptides and a PILIS model *Major changes in functionality:* - Update notification: starting with OpenMS 2.1 all TOPP tools will check for updated versions of the tools online and will print an information message if a newer version is available. This version check occurs only once per day and tool. Information on which tools are executed will be collected anonymously to identify which tools are no longer used and to optimally distribute development resources. If the feature causes problems or concerns, it can be disabled through a command line switch or environment variable (see the documentation and OpenMS wiki). - InternalCalibration: - supports calibration using a table of lock masses and peptide ids. - global or RT-chunked calibration - linear & quadratic models (with intensity weighting) - outlier removal via RANSAC - reoccurring calibrations can be quickly applied to other files using the novel ExternalCalibration tool - OpenSwathWorkflow - support for metabolites / small molecules - MapAlignerIdentification - support for “lowess” transformation model - AccurateMassSearch: - support for multiple databases - FeatureFinderMetabo - isotope spacing model for carbon-rich molecules (e.g. lipids) - PeakPickerHiRes and MassTraceExtractor: - support for FWHM annotation *File formats:* - Improved mzIdentML support (experimental) - Improved pepXML support - Improved support for indexed mzML files - Improved TraML support *Databases:* - By default, decoy sequences are now denoted by a prefix ‘DECOY_’. *Third-party software:* - update for X!Tandem VENGEANCE (2015.12.15) - update for MS-GF+ Release v2016.10.14, released October 14, 2016 - update for pwiz 3.0.9935 |
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From: Timo S. <sac...@gm...> - 2016-09-07 10:30:35
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Dear friends and colleagues, we are happy to announce the 9th OpenMS User Meeting on September 21st -23rd, 2016 at the University of Tübingen, Germany <http://open-ms.sourceforge.net/wp-content/uploads/2015/11/Neckarfront.jpg>( wikipedia.org, Felix König) During the meeting, we will present the capabilities of OpenMS, and discuss your needs and future directions in mass spectrometry. This year’s meeting will include an* optional OpenMS tutorial session on the first day (Wednesday, September 21)* with the *general conference starting on Thursday, September 22*. Traditionally, the schedule of our meetings is very flexible, allowing discussions and contributions from the participants. You can *bring your data*, an OpenMS *wish list*, *ideas for collaboration projects*, and also *give a short (~25 min) talk about your project*. This may include suggestions in areas where currently available software solutions were unsatisfactory. We would be very happy to welcome you in Tübingen this year. *Registration* In order to cover some of the conference costs, we need to charge a small participation fee. Regular participants will need to pay 100€, while students will pay a reduced fee of 75€. Please follow the link to register : OpenMS UM 2016 registration form <https://goo.gl/forms/C8apCLFt7bWOXCN33> (registration deadline extended to September 13) You can find travel information and additional details on our homepage: http://www.openms.de/um2016/ Contact sac...@in... – scientific and program questions See you in Tübingen! The OpenMS Team |
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From: Timo S. <sac...@gm...> - 2016-08-18 07:47:18
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Dear friends and colleagues, we are happy to announce the 9th OpenMS User Meeting on September 21st -23rd, 2016 at the University of Tübingen, Germany <http://open-ms.sourceforge.net/wp-content/uploads/2015/11/Neckarfront.jpg>( wikipedia.org, Felix König) During the meeting, we will present the capabilities of OpenMS, and discuss your needs and future directions in mass spectrometry. This year’s meeting will include an* optional OpenMS tutorial session on the first day (Wednesday, September 21)* with the *general conference starting on Thursday, September 22*. Traditionally, the schedule of our meetings is very flexible, allowing discussions and contributions from the participants. You can *bring your data*, an OpenMS *wish list*, *ideas for collaboration projects*, and also *give a short (~25 min) talk about your project*. This may include suggestions in areas where currently available software solutions were unsatisfactory. We would be very happy to welcome you in Tübingen this year. *Registration* In order to cover some of the conference costs, we need to charge a small participation fee. Regular participants will need to pay 100€, while students will pay a reduced fee of 75€. Please follow the link to register : OpenMS UM 2016 registration form <https://goo.gl/forms/C8apCLFt7bWOXCN33> (registration closes September 4) You can find travel information and additional details on our homepage: http://www.openms.de/um2016/ Contact sac...@in... – scientific and program questions See you in Tübingen! The OpenMS Team |
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From: Julianus P. <pfe...@in...> - 2016-04-27 08:57:30
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We are proud to announce the next source-only OpenMS release (version 2.0.1) with major additions and bug fixes. Download <https://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.0.1/> For up-to-date install instructions please refer to the documentation <http://ftp.mi.fu-berlin.de/pub/OpenMS/release2.0.1-documentation/html/index.html>. CHANGELOG For details on resolved issues and merged features please see our GitHub page <https://github.com/OpenMS/OpenMS/issues?utf8=%E2%9C%93&q=is:closed+>. A full list of changed tool parameters can be found in the released CHANGELOG <https://github.com/OpenMS/OpenMS/blob/Release2.0.1/CHANGELOG>. OpenMS 2.0.1 is a source-only release of the core libraries and tools. This means that although we released the automatically generated installers for your convenience, we denote that these are not fully supported/tested. The same holds for the use of our provided tools in the third-party workflow systems for which we established integration (e.g. KNIME, ProteomeDiscoverer/CompoundDiscoverer). Our team of developers is happy to help you with any issues you might encounter. In such a case, please write to the mailing list <mailto:ope...@li...> or submit an issue on our GitHub issue tracker <https://github.com/OpenMS/OpenMS/issues>. Stabilisation of the interaction with third-party tools and workflow systems is scheduled for the next major release. Nonetheless, with over 300 merged pull requests, this source-only release introduces a considerable number of new features, bug fixes and speed improvements. Notable changes are: File formats: Improved mzIdentML support (experimental) Improved mzTab support (experimental) Comet pepXML file reading support (experimental) Search parameter units are retained through id files Faster base64 decoding in XML files Databases: HMDB has been updated to version 3.6 TOPPView: Added slight margin around data range (%2) for improved visualization Added FeatureFinderMultiplex to the tools accessible from TOPPView Some fixes to the scrollbar behaviour Added tools: IDScoreSwitcher -- Switches between different scores of peptide or protein hits in identification data (UTIL) LuciphorAdapter -- Modification site localisation using LuciPHOr2 (TOPP) MetaProSIP -- Performs proteinSIP on peptide features for elemental flux analysis (UTIL) MzMLSplitter -- Splits an mzML file into multiple parts (UTIL) OpenSwathAssayGenerator -- Generates assays according to different models for a specific TraML (TOPP) Removed tools: RTAnnotator -- Annotates identification files that are missing the RT field (UTIL) Tools with major changes: OpenSWATH now outputs peak apices Improved iRT correction Assay generator UIS scoring Deuterium labeling in MetaProSIP (experimental) XTandemAdapter allows for external config file TextExporter can optionally export PeptideIdentification and PeptideHits meta-values FeatureLinkerUnlabeledQT speed improvements FileMerger allows to concatenate files in RT MzTabExporter supports protein IDs PeakPickerWavelet speedup HiResPrecursorMassCorrector supports correction of precursors to detected features FeatureFinderMultiplex speed improvements Library: Support for user definable enzymes available in EnzymesDB.xml PeptideIndexing is now available as internal algorithm EnzymaticDigestion allows for minimum / maximum length constraints HyperScore and PScore implementations Fits allow extrapolation of data values QT clustering is now order independent Additional convinience functions to access the nearest spectrum peak in a mass tolerance window User defined averagine compositions A fast linear lowess implementation has been added MetaInfoInterface has been added to FeatureMap to store additional meta-values Calculation of Median Absolute Deviation General: OpenMS writes indexed mzML by default OpenMS home directory can be configured through OPENMS_HOME_DIR environment variable Updated GenericWrapper definitions for MS-GF+ and Mascot Third-party software: LuciphorAdapter (experimental) PTM localization using the LuciPHOr2 algorithm (http://luciphor2.sourceforge.net/ <http://luciphor2.sourceforge.net/>) |
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From: Johannes V. <ve...@in...> - 2016-02-18 19:09:24
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Dear OpenMS Community, We are happy to announce the release of the newest version 2.0.2 of our OpenMS Community Nodes for Thermo Proteome Discoverer! It contains a number of great improvements and critical bug fixes and we strongly encourage users of earlier versions to update! You'll find it at http://openms.de/pd Highlights: - LFQProfiler: - Significant speedup of feature detection algorithm (30-50x!) - Now using a better RT alignment algorithm supporting non-linear transformations - Protein-level FDR filtering before protein quantification - Choose intensity normalization method (median, quantile, none) - Option to normalize using only a subset of the features (e.g., house-keeping proteins) - Prefiltering Fido input makes Fido much faster - Choose which m/z value to use for ID mapping: precursor or computed from peptide sequence - Various bug fixes, e.g. unique peptide quantification, path names containing commas - RNPxl: - Advanced parameter “Fragment adducts” allows low-level customization of the fragmentation chemistry - Bug fixes - General: - We now offer a manual installation package for the reported cases where the installer could not find the PD registry key and hence could not determine where to install the nodes - Improved documentation: installation instructions and user manual Best regards, Hannes on behalf of the OpenMS team |
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From: Johannes V. <ve...@in...> - 2015-12-11 17:47:29
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Dear OpenMS Community, We are happy to announce the release of the newest version 2.0.1 of our OpenMS Community Nodes for Thermo Proteome Discoverer! It contains a number of improvements and critical bug fixes and is the first release to support Proteome Discoverer 2.1! You'll find it at http://openms.de/pd Highlights: - RNPxl now features an interactive fragment spectrum visualization widget - Uses an up-to-date version of OpenMS (faster algorithms) - Improved stability - Support for PD 2.1 Best regards, Hannes |
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From: Timo S. <sac...@gm...> - 2015-05-21 12:58:05
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Dear friends of OpenMS, we are happy to announce the 8th OpenMS User Meeting from *September 16th-18th 2015 at the Medizinisches Proteom-Center in Bochum*. During the meeting we will present the capabilities of OpenMS, and discuss your needs and future directions in mass spectrometry. This year’s meeting will include an* optional OpenMS tutorial session on the first day (Wednesday)* with the *general conference starting on Thursday, September 17*. Traditionally, the schedule of our meetings is very flexible, allowing discussions and contributions from the participants. You can bring your data, an OpenMS wish list, ideas for collaboration projects, and also *give a talk* about your project. This may include suggestions in areas where currently available software solutions were unsatisfactory. We would be very happy to welcome you in Bochum this year. Please register as soon as possible for the OpenMS user meeting at http://open-ms.sourceforge.net/um2015/ Best regards, The OpenMS team |
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From: Timo S. <sac...@gm...> - 2015-04-11 20:38:29
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We are proud to announce the next major OpenMS release (version 2.0) with many internal changes, major additions and bug fixes. *Download <https://sourceforge.net/projects/open-ms/files/OpenMS/OpenMS-2.0/>* For install instructions please refer to the documentation <http://ftp.mi.fu-berlin.de/pub/OpenMS/release2.0-documentation/html/index.html> *CHANGELOG* *For a full list of resolved issues and changed tool parameters please refer to the CHANGELOG <https://github.com/OpenMS/OpenMS/blob/master/CHANGELOG>.* OpenMS 2.0 is the first release after the switch to git and a complete overhaul of the build system. It introduces a considerable number of new features and bug fixes. Furthermore, we removed the dependency to GSL and replaced the functionality using Eigen3 and Wildmagic. Thus, the OpenMS core and the full build are now under a more permissive non-GPL (e.g., Apache or BSD) license. *File formats:*- mzQuantML support (experimental) - mzIdentML support (experimental) - mzTab support (experimental) - Indexed mzML support - Support for numpress encoding in mzML - Major speed improvement in mzML / mzXML parsing (up to 4x for some setups) *TOPPView*: - Support for visualizing mass fingerprinting hits from featureXML along with their raw spectra in MS1 - Improved “Tools” -> “Goto” dialog – Improved display of m/z, RT, and intensity values 1D and 2D view *New tools*: - FeatureFinderIdentification — Detects features in MS1 data based on peptide identifications (TOPP) - FeatureFinderMultiplex — Determination of peak ratios in LC-MS data (TOPP) for e.g. SILAC or Dimethyl labeling - FidoAdapter — Runs the protein inference engine Fido (TOPP) - LowMemPeakPickerHiRes — Finds mass spectrometric peaks in profile mass spectra (UTIL) - LowMemPeakPickerHiRes_RandomAccess — Finds mass spectrometric peaks in profile mass spectra (UTIL) - MRMTransitionGroupPicker (UTIL) - MSGFPlusAdapter — MS/MS database search using MS-GF+ (TOPP) - MetaboliteSpectralMatcher — Find potential HMDB ids within the given mass error window (UTIL) - OpenSwathWorkflow — Complete workflow to run OpenSWATH (UTIL) - PeakPickerIterative — Finds mass spectrometric peaks in profile mass spectra (UTIL) - RTAnnotator — Annotates identification files that are missing the RT field (UTIL) - SimpleSearchEngine — Annotates MS/MS spectra using SimpleSearchEngine (UTIL) - TopPerc — Facilitate input to Percolator and reintegrate (UTIL) *Deprecated tools: * - DBExporter — Exports data from an OpenMS database to a file (TOPP) - DBImporter — Imports data to an OpenMS database (TOPP) - FeatureFinderRaw — Determination of peak ratios in LC-MS data (TOPP) - SILACAnalyzer — Determination of peak ratios in LC-MS data (TOPP) *Status changes: * - PhosphoScoring (UTIL -> TOPP) Tools with major changes: - OpenSWATH now supports MS1 extraction and labelled workflows - OpenSWATHWorkflow single binary (high performance integrated workflow) - IsobaricAnalyzer now supports TMT 10-plex *General: * - Removed GSL dependencies – Introduced low memory versions of various algorithms - OpenMS now offers a single interface for different implementations to access mass spectrometric data - in memory - on disk with index – cached on disc for fast access as well as a chainable, low memory sequential processor of MS data (using a separate interface) - pyOpenMS now supports python 3.x - Refactored AASequence, major speed improvement (~40x) for construction of unmodified sequences *Third party software:* - Added Fido support - Added MS-GF+ support *Changes to the Build System / Package System: * - Restructured repository layout and build system - Added support for Travis CI - Simplified pyOpenMS build system - Support for Visual Studio 2013 |