galaxy-proteomics

galaxy-proteomics@lists.galaxyproject.org

20 discussions

Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy Workshop?
by Pratik Jagtap 31 May '14

31 May '14

Hello Dave, Thanks for the mail. The Galaxy-P 101<https://usegalaxyp.readthedocs.org/en/latest/sections/galaxyp_101.html> was written and used by us (John Chilton and myself) in November 2012 and it was last tested in July 2013. It will be great if anyone has an opportunity to see if and how it works. There is a need for a new GalaxyP 101 - which we will do so after we have new set of tools such as MS-GF+ and PeptideShaker installed. As we publish, we will also have pages and tutorials for proteogenomics and metaproteomics workflows. *> Galaxy-P folks*: How do you feel about others using the Galaxy-P 101 in > workshops? I can imagine installing all the tools on the workshop servers > (in which case it seems like an easy win), or running directly off Galaxy-P (which would better highlight Galaxy-P, but put a load on your servers). Once tested, I think it is a good idea to have GalaxyP101 on the workshop servers. For most of our proteomics work - we have been using ProteinPilot ( a Windows-based commercial tool). We have a webinar available in case users are interested - z.umn.edu/ppingp Thanks and Regards, Pratik Pratik Jagtap, Managing Director, Center for Mass Spectrometry and Proteomics, 43 Gortner Laboratory 1479 Gortner Avenue St. Paul, MN 55108 Phone: 612-624-9275 On Fri, May 23, 2014 at 11:54 AM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hi Pratik and JJ, > > Just a heads up that there's a relevant thread on the Galaxy-Proteomics > list that you might want to respond to. > > Bart is on the list, but I don't think either of you are. If you respond, > please respond on-list, if you are comfortable with that. > > Thanks, > > Dave C > > > > ---------- Forwarded message ---------- > From: Dave Clements <clements(a)galaxyproject.org> > Date: Fri, May 23, 2014 at 9:52 AM > Subject: Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy > Workshop? > To: Ira Cooke <I.Cooke(a)latrobe.edu.au> > Cc: Galaxy Proteomics List <galaxy-proteomics(a)lists.bx.psu.edu> > > > Hi Ira, > > Thanks for the pointer. And many thanks to the Galaxy-P folks for > creating this. In hindsight (which I'm *really* good at), Galaxy-P seems > an obvious place to look for this. > > The example looks enormous, but it's well documented. I'll give it a > careful look. > > And, for this workshop and for future reference: > > *Galaxy-P folks*: How do you feel about others using the Galaxy-P 101 in > workshops? I can imagine installing all the tools on the workshop servers > (in which case it seems like an easy win), or running directly off Galaxy-P > (which would better highlight Galaxy-P, but put a load on your servers). > > Thanks again, > > Dave C. > > > > > On Thu, May 22, 2014 at 5:36 PM, Ira Cooke <I.Cooke(a)latrobe.edu.au> wrote: > >> Hi Dave, >> >> I haven’t gone through it myself, but this looks good >> >> https://usegalaxyp.readthedocs.org/en/latest/sections/galaxyp_101.html >> >> Cheers >> Ira >> >> >> On 23 May 2014, at 5:11 am, Dave Clements <clements(a)galaxyproject.org> >> wrote: >> >> Hello all, >> >> Does anyone know of worked proteomics analysis that I could use for a >> Galaxy workshop? I'm giving a workshop in July and the hosts are >> interested in proteomics. I did tell them I currently have no knowledge of >> proteomics, so they aren't expecting me to cover it. However, if a ready >> made example is out there, I might be able to come up to speed on the >> basics before then >> >> Thanks, >> >> Dave C >> >> -- >> http://galaxyproject.org/GCC2014 >> http://galaxyproject.org/ >> http://getgalaxy.org/ >> http://usegalaxy.org/ >> https://wiki.galaxyproject.org/ >> _______________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> >> >> > > > -- > http://galaxyproject.org/GCC2014 > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ > > > > -- > http://galaxyproject.org/GCC2014 > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > https://wiki.galaxyproject.org/ >

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Re: [galaxy-proteomics] Worked Proteomics Example for a Galaxy Workshop?
by Ira Cooke 23 May '14

23 May '14

Hi Dave, I haven’t gone through it myself, but this looks good https://usegalaxyp.readthedocs.org/en/latest/sections/galaxyp_101.html Cheers Ira On 23 May 2014, at 5:11 am, Dave Clements <clements(a)galaxyproject.org<mailto:clements@galaxyproject.org>> wrote: Hello all, Does anyone know of worked proteomics analysis that I could use for a Galaxy workshop? I'm giving a workshop in July and the hosts are interested in proteomics. I did tell them I currently have no knowledge of proteomics, so they aren't expecting me to cover it. However, if a ready made example is out there, I might be able to come up to speed on the basics before then Thanks, Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ _______________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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Move to Google Groups
by Dave Clements 23 May '14

23 May '14

Hello Galaxy Proteomicists! The Galaxy Project has started to create new mailing lists using a Google Groups infrastructure. The new lists still work like mailing lists (plus other stuff). We are hoping that Google Groups proves to be less maintenance than Mailman. We are also considering moving our established lists to Google too. Since this is the smallest and least active of the Galaxy community's mailing lists, this is the first established list we are going to move. Look for this to happen before GCC2014. If anyone has any requests or questions about the move, please let us know. Thanks, Dave C PS: John Chilton originally wanted this list set up on Google Groups. I talked him out of it. There can't possibly be a lesson for me in that experience, can there? ;-) -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Worked Proteomics Example for a Galaxy Workshop?
by Dave Clements 23 May '14

23 May '14

Hello all, Does anyone know of worked proteomics analysis that I could use for a Galaxy workshop? I'm giving a workshop in July and the hosts are interested in proteomics. I did tell them I currently have no knowledge of proteomics, so they aren't expecting me to cover it. However, if a ready made example is out there, I might be able to come up to speed on the basics before then Thanks, Dave C -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Fwd: [bioinfo] Post-doctoral position in computational mass spectrometry at CEA Saclay (France, Paris area)
by Dave Clements 16 Apr '14

16 Apr '14

Hello all, Forwarding this from SFBI list. Dave C ---------- Forwarded message ---------- From: <etienne.thevenot(a)cea.fr> Date: Tue, Apr 15, 2014 at 1:07 AM Subject: [bioinfo] Post-doctoral position in computational mass spectrometry at CEA Saclay (France, Paris area) To: bioinfo(a)sfbi.fr Innovative algorithms and software tools for spectra interpretation and structure elucidation in metabolomics Background The Laboratory for Data Analysis and Smart Systems (LADIS) at CEA (French Alternative Energies and Atomic Energy Commission) has strong expertise in processing and analysis of mass spectrometry (MS) data and has a longstanding partnership with Laboratory of Drug Metabolism (LEMM) which is specialized in LC-MS metabolomics. Together with three INRA platforms (PFEM, BMP and MetaToul at Clermont-Ferrand, Bordeaux and Toulouse, respectively), we develop the bioinformatics tools for MetaboHUB, the national infrastructure in metabolomics and fluxomics (www.metabohub.fr/en). The three main tasks are: 1) developing a Galaxy workflow for data processing, analysis and annotation (in collaboration with the French Institute for Bioinformatics), 2) building a reference database for compounds and spectra (NMR and MS) with the corresponding tools for spectra visualization, matching and interpretation, and 3) managing the data and metadata resulting from the analysis of samples from large cohorts on the four platforms. As metabolomics is increasingly used for biomarker discovery, high-throughput annotation of MS peak signals is critical. Within task 2, the development of efficient algorithms for mass spectra interpretation is tightly coupled to the building of a comprehensive database of high quality spectra. Whereas software tools exist for the determination of the chemical formula (based on mass accuracy, analysis of isotope distribution, etc.), the elucidation of de novo structures (i.e. from unknown compounds) through interpretation of fragmentation spectra (MS/MS) remains challenging due to the chemical diversity of metabolites. Such a task requires the ability to develop efficient combinatorial algorithms and interactive visualization tools in addition to a good knowledge of both the rules of ionization and fragmentation in the gas phase. Project Within the MetaboHUB project, the post holder will develop the software tools to interpret MS/MS spectra and determine the structure of previously uncharacterized compounds. He/she will work with Pr. Jean-Claude Tabet to automate the process of spectrum interpretation by 1) determining the metadata regarding spectrum acquisition to be stored in the database, 2) designing and implementing the algorithms for MS and MS/MS spectra matching, chemical structure elucidation and visualization, and 3) integrating the tools in the MetaboHUB database. In addition, the post holder will contribute to task 3 by benchmarking software tools and architecture solutions for collaborative management of the huge amount of raw and processed data generated simultaneously by the four MetaboHUB platforms. Profile The successful candidate should hold a PhD in cheminformatics, bioinformatics or computer science and have a strong understanding of organic chemistry. The candidate is expected to have experience with Java and C++, with database management systems (MySQL) and with web content management systems (jQuery). The candidate should have presented his/her Ph.D. thesis for less than two years before the starting date and should have a good record of scientific publications. Our offer 1-year contract (renewable once). Net salary: about 2200 €/month, depending on experience. Application Please send your CV and your letter of motivation to: Etienne Thévenot Laboratory for Data Analysis and Smart Systems CEA, Saclay Center, build. 565 (DRT/LIST/DM2I/LADIS) F-91191 Gif-sur-Yvette Cedex, France Mail: etienne.thevenot(a)cea.fr Website: http://www-centre-saclay.cea.fr/en -- http://www.sfbi.fr Archives : http://listes.sfbi.fr/wws/arc/bioinfo -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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ASMS Abstract Deadline is February 7
by Dave Clements 23 Jan '14

23 Jan '14

Hello all, Last year there was an enormous Galaxy presence at the ASMS conference: https://wiki.galaxyproject.org/Events/ASMS2013 I have no idea if there will be another swarming presence in 2014, but if you are planning to present something then please let me know and I'll do my best to let the world know about it. The abstract deadline is February 7. See http://www.asms.org/conferences/annual-conference/abstract-submission. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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CAPER: A new proteomics Galaxy Server
by Dave Clements 06 Dec '13

06 Dec '13

Hello all (proteomaticians?), Please welcome a new public Galaxy server to the Galaxy proteomics community: CAPER <http://www.bprc.ac.cn/CAPE>: An Interactive, Configurable, and Extensible Workflow-Based Platform to Analyze Data Sets from the Chromosome-centric Human Proteome Project. The full entry from the http://wiki.galaxyproject.org/PublicGalaxyServerspage is below. There are online tutorials, and email support is offered by Dong Li and Dan Wang, both CC'd here. Also, please tell them what a spectacularly great email list this is, so that they will subscribe to it. ;-) Happy December! Dave C CAPER [image: CAPER] <http://www.bprc.ac.cn/CAPE> - *Links:* - CAPER <http://www.bprc.ac.cn/CAPE> at Beijing Proteome Research Center<http://www.bprc.ac.cn/>, China - "CAPER 2.0: An Interactive, Configurable, and Extensible Workflow-Based Platform to Analyze Data Sets from the Chromosome-centric Human Proteome Project <http://pubs.acs.org/doi/abs/10.1021/pr400795c>" by Wang, *et al.*, *J. Proteome Res.*, DOI: 10.1021/pr400795c, Publication Date (Web): November 22, 2013 - *Domain/Purpose:* - "An Interactive, Configurable, and Extensible Workflow-Based Platform to Analyze Data Sets from the Chromosome-centric Human Proteome Project <http://www.c-hpp.org/>" - *Comments:* - The Chromosome-centric Human Proteome Project (C-HPP) aims to map and annotate the entire human proteome by the "chromosome-by-chromosome" strategy. As the C-HPP proceeds, the increasing volume of proteomic data sets presents a challenge for customized and reproducible bioinformatics data analyses for mining biological knowledge. To address this challenge CAPER 2.0 - an interactive, configurable and extensible workflow-based platform is developed for C-HPP data analyses. In addition to the previous visualization functions of track-view and heatmap-view<http://pubs.acs.org/doi/abs/10.1021/pr300831z>, CAPER 2.0 presents a powerful toolbox for C-HPP data analyses and also integrates a configurable workflow system that supports the view, construction, edit, run, and share of workflows. These features allow users to easily conduct their own C-HPP proteomic data analyses and visualization by CAPER 2.0. CAPER 2.0 now presents four specific workflows for finding missing proteins, mapping peptides to chromosomes for genome annotation, integrating peptides with transcription factor binding sites from ENCODE data sets, and functionally annotating proteins. - *User Support:* - Tutorials<http://61.50.138.124/caper2/static/documentation/index.html> - Email: Dong Li <lidong.bprc(a)foxmail.com>, Dan Wang<wangdanburnett(a)163.com> - *Quotas:* - Free for academic users. Creating an account is recommended. - *Sponsor(s):* - Beijing Proteome Research Center (BPRC) <http://www.bprc.ac.cn/>, the Human Liver Proteome Project (HLPP)<http://www.hupo.org/initiatives/human-liver-proteome-project/>, and the Chromosome-centric Human Proteome Project (C-HPP)<http://www.c-hpp.org/> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Re: [galaxy-proteomics] ASMS Follow Up
by Bart Gottschalk 24 Oct '13

24 Oct '13

What version of Galaxy did you clone and are running when you get this error? http://bitbucket.org/galaxy/galaxy-central/ http://bitbucket.org/galaxy/galaxy-dist/ http://bitbucket.org/galaxyp/galaxyp-central/ Once we have this answer we can help you debug the error. On Mon, Oct 21, 2013 at 8:25 AM, John Chilton <chil0060(a)umn.edu> wrote: > > > ---------- Forwarded message ---------- > From: Gerben Menschaert <gerben.menschaert(a)gmail.com> > Date: Mon, Oct 21, 2013 at 4:40 AM > Subject: Re: ASMS Follow Up > To: John Chilton <chil0060(a)umn.edu> > > > Hello John Mitchel, > > I hope you can help out. > PeptideShaker used to be on our Galaxy-P environment, but I removed it. > I'm trying to re-install it again from the toolshed. > > While doing so, I bumped into the following error (see below). > > Could you point me in the good directory. > > > Many thanks in advance, > Gerben Menschaert > > > PS: Also, is there a special GALAXY-P user/development mailing list? > > > ⇝ KeyError: 'tool_panel_section' > URL: > http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to… > Module weberror.evalexception.middleware:*364* in respond <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > app_iter *=* self*.*application*(*environ*,* detect_start_response*)* > Module paste.recursive:*80* in __call__ <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > *return* self*.*application*(*environ*,* start_response*)* > Module paste.httpexceptions:*633* in __call__ <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > *return* self*.*application*(*environ*,* start_response*)* > Module galaxy.web.framework.base:*132* in __call__ <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > *return* self*.*handle_request*(* environ*,* start_response *)* > Module galaxy.web.framework.base:*190* in handle_request <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > body *=* method*(* trans*,* ****kwargs *)* > Module galaxy.web.framework:*221* in decorator <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* > Module galaxy.webapps.galaxy.controllers.admin_toolshed:*850* in > prepare_for_install <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > repository_util*.*handle_tool_shed_repositories*(* trans*,* > installation_dict*,* using_api*=*False *)* > Module tool_shed.galaxy_install.repository_util:*338* in > handle_tool_shed_repositories <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > new_tool_panel_section*=*new_tool_panel_section *)* > Module tool_shed.util.repository_dependency_util:*149* in > create_repository_dependency_objects <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > common_install_util*.*activate_repository*(* trans*,* > installed_tool_shed_repository *)* > Module tool_shed.util.common_install_util:*36* in activate_repository > <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_to…> > tool_panel_dict *=* repository*.*metadata*[* 'tool_panel_section' *]* > *KeyError: 'tool_panel_section'* > * > * > > > > > On Jun 17, 2013, at 4:52 PM, John Chilton <chil0060(a)umn.edu> wrote: > > On behalf of myself and my colleague Jim Johnson, I wanted to thank > you for dropping by one or both of our posters. You can find digital > copies of both poster below. > > "Reproducible Proteomic Workows using Extensions to the Galaxy Framework" > http://getgalaxyp.org/documents/asms2013_galaxy_extensions.pdf > > "Building Proteomic Application Platforms for Cloud Computing > Environments with CloudBioLinux" > http://getgalaxyp.org/documents/asms2013_cloud_computing.pdf > > We had a great time last Monday and agree that a lot of good ideas > were generated. If you have specific questions, comments, or > suggestions please do not hesitate to drop us a line. (I have cc'ed > Jim Johnson, as well Dr. Pratik Jagtap the Galaxy-P project manager, > Dr. Ben Lynch the head of application development at MSI, and Dr. > Timothy Griffin the principle investigator for Galaxy-P on this > e-mail. Feel free to direct questions to whomever you feel is most > appropriate.) > > You can find more information about Galaxy-P at http://getgalaxyp.org/ > and try our public server at https://usegalaxyp.org/. You can find > more information about Galaxy more broadly at > http://galaxyproject.org/ and CloudBioLinux at > http://cloudbiolinux.org/. All of our source code is open source and > available at various places on BitBucket and GitHub, if you are > interested in any particular part of what we have done let me know > which and I can point you to it. > > Thanks again, > -John > > ------------------------------------------------ > John Chilton > Senior Software Developer > University of Minnesota Supercomputing Institute > Office: 612-625-0917 > Cell: 612-226-9223 > > > >

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Proteomics on Public Galaxy Servers
by Dave Clements 02 Oct '13

02 Oct '13

Hello all, There was something buries in the October Galaxy Update newsletter that just went out that might be of interest to this group. One of the new public Galaxy servers has several proteomics tools on it: USP-FCFRP [image: Laboratory of Biological Physics at USP-FCFRP]<http://fisbio.fcfrp.usp.br:8080/> - *Link:* - Laboratory of Biological Physics at USP-FCFRP<http://fisbio.fcfrp.usp.br:8080/> - *Domain/Purpose:* - Summary of the currently available tools: - *ProtPred-GROMACS*: *Ab initio* protein structure prediction framework which uses evolutionary algorithms to optimize objective functions such as potential energy, number of hydrogen bonds and solvent accessible surface area. - 2PG: Faster and simpler algorithm in which one objective function is optimized 3PG: A more robust approach in which multiple objective functions are optimized at the same time *Protein Validation*: Check the integrity of a PDB file *Protein Desolvation*: Remove a solvation layer around your protein. - *Comments:* - *User Support:* - Laboratory of Biological Physics <http://fisbio.fcfrp.usp.br/> - *Quotas:* - "You can use tools developed at our laboratory and by our colaborators for free. You just need to sign up to the server using your academic e-mail." - *Sponsor(s):* - Laboratory of Biological Physics <http://fisbio.fcfrp.usp.br/>, part of the Faculty of Pharmaceutical Sciences of Ribeirão Preto (FCFRP)<http://www.fcfrp.usp.br/> at the University of São Paulo (USP) <http://www.usp.br/>. And, while I'm here, there are also a couple of other public sites that feature proteomics prominently: 1. Galaxy-P <http://wiki.galaxyproject.org/PublicGalaxyServers#Galaxy-P> 2. GWIPS-vi <http://wiki.galaxyproject.org/PublicGalaxyServers#GWIPS-viz> z 3. SymD <http://wiki.galaxyproject.org/PublicGalaxyServers#SymD> (not up currently) Hope this interesting. If it isn't, please let me know. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Welcome
by Ira Cooke 11 Jun '13

11 Jun '13

Welcome to the Galaxy Proteomics mailing list. This list is to facilitate discussion about proteomics tools in Galaxy. The scope of the list includes development of new tools, issues encountered with existing tools and announcements about related workshops or resources. To kick off, here are some announcements; 1. There will be a workshop on Galaxy in Proteomics tonight at 5:45 at ASMS 2013 in Minneapolis. 2. Ira Cooke has published instructions on setting up a base bones virtual machine ready to install Galaxy Proteomics tools at; https://bitbucket.org/iracooke/protk_vagrant

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