galaxy-proteomics

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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/

3 2

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: > 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> Module weberror.evalexception.middleware:*364* in respond 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> 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> >> 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> app_iter *=* self*.*application*(*environ*,* detect_start_response*)* > Module paste.recursive:*80* in __call__ 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> 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> >> 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> *return* self*.*application*(*environ*,* start_response*)* > Module paste.httpexceptions:*633* in __call__ 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> 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> >> 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> *return* self*.*application*(*environ*,* start_response*)* > Module galaxy.web.framework.base:*132* in __call__ 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> view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_tools_for_display_in_tool_panel=True&encoded_repo_info_dicts=90a33e331bc412ca17eb74a9796d006a4cb070ce%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&includes_tools=True&tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=True#> > >> 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> *return* self*.*handle_request*(* environ*,* start_response *)* > Module galaxy.web.framework.base:*190* in handle_request 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> 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> >> 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> body *=* method*(* trans*,* ****kwargs *)* > Module galaxy.web.framework:*221* in decorator 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> 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> >> 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> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* > Module galaxy.webapps.galaxy.controllers.admin_toolshed:*850* in > prepare_for_install 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> 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> >> 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> 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 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> view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_tools_for_display_in_tool_panel=True&encoded_repo_info_dicts=90a33e331bc412ca17eb74a9796d006a4cb070ce%3A7b22706570746964657368616b6572223a205b2254686973207265706f7369746f727920636f6e7461696e73206120746f6f6c20746861742077726170732053656172636847554920616e6420506570746964655368616b65722e20222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f67616c617879702f706570746964657368616b6572222c2022313836666463346233333130222c20223136222c202267616c61787970222c207b22726f6f745f6b6579223a2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564755f5f455345505f5f706570746964657368616b65725f5f455345505f5f67616c617879705f5f455345505f5f3138366664633462333331305f5f455345505f5f46616c7365222c20226465736372697074696f6e223a202252657175697265642070726f74656f6d69637320646570656e64656e636965732e222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564755f5f455345505f5f706570746964657368616b65725f5f455345505f5f67616c617879705f5f455345505f5f3138366664633462333331305f5f455345505f5f46616c7365223a205b5b22687474703a2f2f746f6f6c736865642e67322e62782e7073752e656475222c202270726f74656f6d6963735f646174617479706573222c2022697261636f6f6b65222c2022663734323930623133366663222c202246616c7365225d2c205b22687474703a2f2f746f6f6c736865642e67322e62782e7073752e656475222c20227061636b6167655f7365617263686775695f315f31345f34222c202267616c61787970222c2022363764653531643532393037222c202246616c7365225d2c205b22687474703a2f2f746f6f6c736865642e67322e62782e7073752e656475222c20227061636b6167655f706570746964657368616b65725f305f32305f31222c202267616c61787970222c2022636664353562366334666132222c202246616c7365225d5d7d2c207b22706570746964655f7368616b65722f302e32302e31223a207b227265706f7369746f72795f6e616d65223a2022706570746964657368616b6572222c20226e616d65223a2022706570746964655f7368616b6572222c202276657273696f6e223a2022302e32302e31222c20227265706f7369746f72795f6f776e6572223a202267616c61787970222c20226368616e67657365745f7265766973696f6e223a2022313836666463346233333130222c202274797065223a20227061636b616765227d2c20227365617263686775692f312e31342e31223a207b227265706f7369746f72795f6e616d65223a2022706570746964657368616b6572222c20226e616d65223a2022736561726368677569222c202276657273696f6e223a2022312e31342e31222c20227265706f7369746f72795f6f776e6572223a202267616c61787970222c20226368616e67657365745f7265766973696f6e223a2022313836666463346233333130222c202274797065223a20227061636b616765227d7d5d7d&includes_tools=True&tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=True#> > >> 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> new_tool_panel_section*=*new_tool_panel_section *)* > Module tool_shed.util.repository_dependency_util:*149* in > create_repository_dependency_objects 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> view<http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_tools_for_display_in_tool_panel=True&encoded_repo_info_dicts=90a33e331bc412ca17eb74a9796d006a4cb070ce%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&includes_tools=True&tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=True#> > >> <http://localhost:8081/galaxy/admin_toolshed/prepare_for_install?includes_tools_for_display_in_tool_panel=True&encoded_repo_info_dicts=90a33e331bc412ca17eb74a9796d006a4cb070ce%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&includes_tools=True&tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&includes_tool_dependencies=True#> > common_install_util*.*activate_repository*(* trans*,* > installed_tool_shed_repository *)* > Module tool_shed.util.common_install_util:*36* in activate_repository > 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> 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> >> 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> 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 01 Oct '13

01 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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