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From: Egon W. <ego...@gm...> - 2018-08-24 07:33:47
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Dear Vidhya, can you please check this StackExchange question and answers? It has the same exit error code 13: https://stackoverflow.com/questions/11461607/cant-start-eclipse-java-was-started-but-returned-exit-code-13 It could be that you have a mismatch of 32/64 bit operating system, Java installation, and/or Bioclipse. Can you please check they are all 32bit or all 64bit? Does that solve your problem? With kind regards, Egon On Thu, Aug 23, 2018 at 4:01 PM Vidhya Iyer <vi...@gm...> wrote: > Hello, > > I would like to use the Bioclipse software for some studies. I have a > Windows 10 OS (64 bit) and downloaded the zip folder and extracted the > files. But even after I clicked on the .exe files, I was not able to see > the blue Welcome page shown in > http://priede.bf.lu.lv/ftp/pub/TIS/kjiimija/Bioclipse/GettingStarted.pdf. > I know I have Java on my OS as I am able to run other Java-based files. > Could you help me resolve this? > > Regards, > > Vidhya Iyer > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Bioclipse-users mailing list > Bio...@li... > https://lists.sourceforge.net/lists/listinfo/bioclipse-users > -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: https://www.zotero.org/egonw ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> ImpactStory: https://impactstory.org/u/egonwillighagen |
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From: Vidhya I. <vi...@gm...> - 2018-08-23 07:06:31
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Hello, I would like to use the Bioclipse software for some studies. I have a Windows 10 OS (64 bit) and downloaded the zip folder and extracted the files. But even after I clicked on the .exe files, I was not able to see the blue Welcome page shown in http://priede.bf.lu.lv/ftp/pub/TIS/kjiimija/Bioclipse/GettingStarted.pdf. I know I have Java on my OS as I am able to run other Java-based files. Could you help me resolve this? Regards, Vidhya Iyer |
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From: Egon W. <ego...@gm...> - 2017-10-21 06:55:13
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Hi Denise, I have pushed a new ChEBI-156-based ontology mapper plugin to the bioclipse.metabolomics repository... please let me know if it behaves as expected. Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/u/egonwillighagen |
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From: Samuel L. <sam...@fa...> - 2016-11-04 10:48:43
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Oops, thanks for pointing this out! We have just updated the wiki and website with info of the release now. Best // Samuel On 2016-11-04 10:07, Peter Maas wrote: > > Interesting but I can’t find any documentation on this update > > Blogs, IRC channels, wiki, home pages and everything else seems > several years old. > > Even in the source files in sourceforge and git commits seem 3 years old. > > But I was able to install and run it. > > Thanks, > > Peter > |
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From: Jonathan A. <jon...@gm...> - 2016-11-04 10:09:53
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On Fri, Nov 4, 2016 at 10:07 AM, Peter Maas <pet...@sp...> wrote: > Interesting but I can’t find any documentation on this update > > Blogs, IRC channels, wiki, home pages and everything else seems several > years old. Hm yea I think blogging activity is down for the moment and I think we have drifted away from IRC as main communicational channel although most of us still hang out there in case someone has questions. Personally I must admit that I haven't done much actual Bioclipse coding in years though. > Even in the source files in sourceforge and git commits seem 3 years old. Yea development no longer takes place on sourceforge. The repositories has moved to Github (https://github.com/bioclipse) -- // Jonathan |
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From: Peter M. <pet...@sp...> - 2016-11-04 09:25:04
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Interesting but I can’t find any documentation on this update Blogs, IRC channels, wiki, home pages and everything else seems several years old. Even in the source files in sourceforge and git commits seem 3 years old. But I was able to install and run it. Thanks, Peter From: Arvid Berg [mailto:gog...@us...] Sent: Thursday, November 03, 2016 6:59 PM To: bio...@li...; Bioclipse-devel ML Subject: [Bioclipse-devel] Bioclipse 2.6.2 released Bioclipse 2.6.2 is now releases and available for download from <https://sourceforge.net/projects/bioclipse/> sourceforge.net This release contains bugfixes and compatibility improvements. // The Bioclipse team |
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From: Arvid B. <gog...@us...> - 2016-11-03 17:59:11
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Bioclipse 2.6.2 is now releases and available for download from sourceforge.net <https://sourceforge.net/projects/bioclipse/> This release contains bugfixes and compatibility improvements. // The Bioclipse team |
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From: jay p. <jay...@gm...> - 2016-08-14 20:25:29
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Hi, I am trying to install Bioclipse-R package, and followed the instruction on this wiki page http://wiki.bioclipse.net/index.php?title=Integrate_R_in_Bioclipse#get_Bioclipse_from_hudson_and_R_from_updatesite since the link for bioclipse 2.5.0 was broken, I went ahead to sourceforge and downloaded the most recent version (2.6.1). I wasnt able to successfully install bioclipse-R package due to dependency issues. The error info is attached below. I'll appreciate any ideas. Thanks, Jay Patel [image: Inline image 1] |
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From: Arvid B. <gog...@us...> - 2016-01-14 17:06:17
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Hi Nick, There is a change in how Windows 10 reports its version to java that is causing troubles in Bioclipse. We have implemented a workaround in our upcoming release, if you go to http://wiki.bioclipse.net/index.php?title=Download you can download Bioclipse "2.6.2 (beta)" for your platform. To be able to install the latest features you need to go to 'Preferences...->Install/Update->Available Software Sites' and change http://update.bioclipse.net to http://devel.bioclipse.net Regards, Arvid 2016-01-06 20:31 GMT+01:00 Nick Price <ni...@te...>: > Hi, > I have recently upgraded to Windows 10 via the Microsoft upgrade system > (not a clean re-install). > I was previously using Windows 7 with Bioclipse running the Decision > support, QSAR, and Opentox extensions. > My "in place" Bioclipse installation refused to acknowledge the presence > of the extensions once windows 10 was running, so I removed Bioclipse, > downloaded the zip file afresh, and started again. Bioslipse installed > fine, and all the extensions and added features installed fine too. > However when Bioclipse was run, none of these extensions were available. > According to Bioclipse, all the extensions were installed but none is > available to use. > I'm sure there's other information you need before you can suggest > what's causing my problems ? > > Regards, > Nick > > -- > Professor N.R.Price. B.A, PhD > Technology for Growth > Oak Lea > Marton > Sinnington > York YO62 6RD > UK > www.technologyforgrowth.co.uk > > "Science and everyday life cannot, and should not be separated" Rosalind > Franklin > > > > > ------------------------------------------------------------------------------ > _______________________________________________ > Bioclipse-users mailing list > Bio...@li... > https://lists.sourceforge.net/lists/listinfo/bioclipse-users > |
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From: Nick P. <ni...@te...> - 2016-01-06 19:51:44
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Hi, I have recently upgraded to Windows 10 via the Microsoft upgrade system (not a clean re-install). I was previously using Windows 7 with Bioclipse running the Decision support, QSAR, and Opentox extensions. My "in place" Bioclipse installation refused to acknowledge the presence of the extensions once windows 10 was running, so I removed Bioclipse, downloaded the zip file afresh, and started again. Bioslipse installed fine, and all the extensions and added features installed fine too. However when Bioclipse was run, none of these extensions were available. According to Bioclipse, all the extensions were installed but none is available to use. I'm sure there's other information you need before you can suggest what's causing my problems ? Regards, Nick -- Professor N.R.Price. B.A, PhD Technology for Growth Oak Lea Marton Sinnington York YO62 6RD UK www.technologyforgrowth.co.uk "Science and everyday life cannot, and should not be separated" Rosalind Franklin |
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From: Egon W. <ego...@gm...> - 2015-12-13 09:33:30
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Hi all, Jena3 has been released and is the way forward. The API has changed a bit, but the core functionality is equivalent and I managed to upgrade this. However, not all current plugins will survive the upgrade. In particular, Pellet will not make the update (along with the OWL manger which used that; use the OWLAPI manager instead), as the current library is no longer open source, and I would have to update the open source version myself (I have no intention too). The new LDF feature may also be temporary be offline, but the authors of that were happy with HDT upgrading, and I expect them to follow soon, so that I can update that too. So, my question to everyone is: is someone depending on Jena2.x in Bioclipse? This would be a good time to let me know. At a rdf manager level nothing will change. Looking forward to hearing from you, greetings, Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen |
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From: Jonathan A. <jon...@gm...> - 2015-07-26 10:08:59
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There is a thread specific container (singleton I think) for the scripting monitors, i.e., the monitor used when running BSL. Don't remember the name of it but I think you just call it with the correct thread and you get the proper monitor. (maybe we should move over to the develop list instead? egonw are you on that?) On Sun, Jul 26, 2015 at 11:24 AM, Egon Willighagen < ego...@gm...> wrote: > On Sat, Jul 25, 2015 at 8:55 PM, Jonathan Alvarsson > <jon...@gm...> wrote: > > I remember thinking about this years ago and then opting for not adding > it. > > Mainly becasue writing the script would be complicated. However, since > you > > want it I don't see any reason for why we should not add it. Remind me, > is > > there a scripting manager yet? Otherrwise I guess it would belong on the > UI > > manager or so... > > There is a js manager, but that is linked to the JavaScript console... > it has stuff like js.say()... in Groovy you can just use "print" so > that was never a problem to me... > > UI sounds appropriate, more than bioclipse, as these messages are > meant for the UI... > > I played with ui.progressMessage(String message, IProgressMonitor > monitor) ... that the monitor that method gets seems different, > because I could not get those message to show up in the GroovyConsole > "monitor"... > > Egon > > > -- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > ORCID: 0000-0001-7542-0286 > ImpactStory: https://impactstory.org/EgonWillighagen > -- // Jonathan |
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From: Egon W. <ego...@gm...> - 2015-07-26 09:24:51
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On Sat, Jul 25, 2015 at 8:55 PM, Jonathan Alvarsson <jon...@gm...> wrote: > I remember thinking about this years ago and then opting for not adding it. > Mainly becasue writing the script would be complicated. However, since you > want it I don't see any reason for why we should not add it. Remind me, is > there a scripting manager yet? Otherrwise I guess it would belong on the UI > manager or so... There is a js manager, but that is linked to the JavaScript console... it has stuff like js.say()... in Groovy you can just use "print" so that was never a problem to me... UI sounds appropriate, more than bioclipse, as these messages are meant for the UI... I played with ui.progressMessage(String message, IProgressMonitor monitor) ... that the monitor that method gets seems different, because I could not get those message to show up in the GroovyConsole "monitor"... Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen |
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From: Jonathan A. <jon...@gm...> - 2015-07-25 18:55:47
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I remember thinking about this years ago and then opting for not adding it. Mainly becasue writing the script would be complicated. However, since you want it I don't see any reason for why we should not add it. Remind me, is there a scripting manager yet? Otherrwise I guess it would belong on the UI manager or so... On Sat, Jul 25, 2015 at 3:33 PM, Egon Willighagen < ego...@gm...> wrote: > Hi all, > > I was wondering if it was possible to add messages to the progress > monitor from the scripting environment? js.say() outputs to the > console, but it would also be nice if I could add info to the process > in the progress view... that way, it would be easier to see how far a > job has progressed, without flooding the scripting console... > > Egon > > -- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > ORCID: 0000-0001-7542-0286 > ImpactStory: https://impactstory.org/EgonWillighagen > > > ------------------------------------------------------------------------------ > _______________________________________________ > Bioclipse-users mailing list > Bio...@li... > https://lists.sourceforge.net/lists/listinfo/bioclipse-users > -- // Jonathan |
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From: Egon W. <ego...@gm...> - 2015-07-25 13:34:06
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Hi all, I was wondering if it was possible to add messages to the progress monitor from the scripting environment? js.say() outputs to the console, but it would also be nice if I could add info to the process in the progress view... that way, it would be easier to see how far a job has progressed, without flooding the scripting console... Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen |
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From: Egon W. <ego...@gm...> - 2015-02-10 08:46:08
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On Mon, Feb 9, 2015 at 10:39 PM, Ola Spjuth <Ola...@fa...> wrote: > This was an old prototype plugin for an early version of Bioclipse that was not ported to v2. I think I remember that it had some basic functionality but that the developer did not finish it. Seconded. I would say the project would need a reboot from scratch... Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen |
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From: Ola S. <Ola...@fa...> - 2015-02-09 21:40:09
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Hi Stephen, This was an old prototype plugin for an early version of Bioclipse that was not ported to v2. I think I remember that it had some basic functionality but that the developer did not finish it. Cheers, Ola On 9 feb 2015, at 20:17, Stephen P. Molnar <s.m...@sb...> wrote: > There s a reference in > http://www.gromacs.org/Downloads/Related_Software/GUI to ' > Bioclipse: there is a plug-in to bioclipse for gromacs, > http://wiki.bioclipse.net/index.php?title=Gromacs_plugin'. > > However, the ULR points back to the Gromos Website. Is there a > bioclipse gromos plugin? If so, where is it? > > Thanks in advance. > > -- > Stephen P. Molnar, Ph.D. Life is a fuzzy set > Foundation for Chemistry Stochastic and Multivariate > www.FoundationForChemistry.com > (614)312-7528(c) > Skype: smolnar1 > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Bioclipse-users mailing list > Bio...@li... > https://lists.sourceforge.net/lists/listinfo/bioclipse-users |
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From: Stephen P. M. <s.m...@sb...> - 2015-02-09 19:17:29
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There s a reference in http://www.gromacs.org/Downloads/Related_Software/GUI to ' Bioclipse: there is a plug-in to bioclipse for gromacs, http://wiki.bioclipse.net/index.php?title=Gromacs_plugin'. However, the ULR points back to the Gromos Website. Is there a bioclipse gromos plugin? If so, where is it? Thanks in advance. -- Stephen P. Molnar, Ph.D. Life is a fuzzy set Foundation for Chemistry Stochastic and Multivariate www.FoundationForChemistry.com (614)312-7528(c) Skype: smolnar1 |
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From: Egon W. <ego...@gm...> - 2015-01-24 11:08:40
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Hi all, I uploaded two Bioclipse scripts to myExperiment.org. 1. create RDF from a TSV file http://www.myexperiment.org/workflows/4582.html 2. run SPARQL queries on Wikidata using Linked Data Fragments http://www.myexperiment.org/workflows/4583.html Grtz, Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen |
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From: Egon W. <ego...@gm...> - 2014-10-28 08:50:02
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Ola, Bart, On Tue, Oct 28, 2014 at 8:46 AM, Ola Spjuth <Ola...@fa...> wrote: > For simpler reports we generate HTML pages that we open in the internal Web > browser in Bioclipse. If there is no manager call to create such a page from > HTML it would be very easy to implement, I can also think of several > convenience methods that would be useful (e.g. shortcuts for creating HTML > snippets and CSS). OK, that sounds like a good way forward. HTML has other advantages too, e.g. that if done well (with RDFa) it can be used to make later summaries (using SPARQL): http://t.co/MkcSCKK1Qq Bart, please have a look at that blog post, and we should discuss shortly ideas about a general HTML(-RDFa) manager to support creating reports in HTML... Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen |
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From: Ola S. <Ola...@fa...> - 2014-10-28 08:07:30
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Hi Egon, For reporting in e.g. Decision Support we use Jasper reports. As I remember it you need to create and design a specific report template (preferably using a report designer such as https://community.jaspersoft.com/project/jaspersoft-studio or http://www.jasperassistant.com/), and then at runtime populate the report with contents programmatically. While it would be possible to populate an existing Jasper report via a manager call, a more general way of creating Jasper reports on the fly would probably be rather difficult. For simpler reports we generate HTML pages that we open in the internal Web browser in Bioclipse. If there is no manager call to create such a page from HTML it would be very easy to implement, I can also think of several convenience methods that would be useful (e.g. shortcuts for creating HTML snippets and CSS). Ola On 27 okt 2014, at 22:11, Egon Willighagen <ego...@gm...<mailto:ego...@gm...>> wrote: Hi all, I have seen some nice reports in the past... I was wondering if those were created using Bioclipse manger calls... That is, is there a manager for creating such reports? Egon ------------------------------------------------------------------------------ _______________________________________________ Bioclipse-users mailing list Bio...@li...<mailto:Bio...@li...> https://lists.sourceforge.net/lists/listinfo/bioclipse-users |
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From: Egon W. <ego...@gm...> - 2014-10-27 21:11:58
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Hi all, I have seen some nice reports in the past... I was wondering if those were created using Bioclipse manger calls... That is, is there a manager for creating such reports? Egon |
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From: Steven W. <SW...@si...> - 2014-08-11 14:28:09
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Hi Valentin, I apologize for not replying sooner . For some reason I didn't get your answer by email and I didn't think to look in the list archives until today. This is what I get when I run the commands you suggested in R: > installed.packages()['rJava','Version'] Error in installed.packages()["rJava", "Version"] : subscript out of bounds > installed.packages()['rj','Version'] Error in installed.packages()["rj", "Version"] : subscript out of bounds My Windows machine is 64-bit. I don't remember which version of Bioclipse I downloaded - 32 or 64-bit. Does it matter? What do you suggest? I looked in the Bioclipse documentation and didn't see anything about specific R packages, although I shouldn't be surprised that it needs rJava installed. Thanks for your help, Steve ------------- Dr. Steven P. Wathen Associate Professor of Chemistry Siena Heights University 1247 East Siena Heights Drive Adrian, MI 49221 (517) 264-7657 sw...@si... |
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From: Valentin G. <val...@fa...> - 2014-07-28 10:29:27
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Hi Steve,
The Bioclipse-R Integration does indeed work with R version 3.1.1.
I suspect your troubles might be related to 32-bit and 64-bit incompatibility. Can you provide some info about your system, Java and Bioclipse - which versions you have, in terms of 32-bit vs 64-bit.
Also, can you check of you have the required R packages installed by running these R commands:
installed.packages()['rj','Version']
installed.packages()['rJava','Version']
Cheers,
Valentin
Valentin Georgiev, PhD
Pharmaceutical Bioinformatics
BMC, Uppsala University
Hello,
I tried to use the Bioclipse R console on my Windows 7 machine and got an error message:
Cannot start the RServi instance.
See http://pele.farmbio.uu.se/bioclipse/help/nav/14_1 or the internal Bioclipse help system!
The latest version of R is 3.1.1, but it looks like the Bioclipse-R integration only works with R v2.15
Are there any plans to update the Bioclipse R support to the current version of R?
I did try installing an earlier version of R and setting the R_HOME field at Bioclipse>Preferences...>R, but the R console still does not work.
Thanks,
Steve
-------------
Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221
(517) 264-7657
swathen@...
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From: Steven W. <SW...@si...> - 2014-07-26 19:36:42
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Hello,
I tried to use the Bioclipse R console on my Windows 7 machine and got an error message:
Cannot start the RServi instance.
See http://pele.farmbio.uu.se/bioclipse/help/nav/14_1 or the internal Bioclipse help system!
The latest version of R is 3.1.1, but it looks like the Bioclipse-R integration only works with R v2.15
Are there any plans to update the Bioclipse R support to the current version of R?
I did try installing an earlier version of R and setting the R_HOME field at Bioclipse>Preferences...>R, but the R console still does not work.
Thanks,
Steve
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Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221
(517) 264-7657
sw...@si...
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