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
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*Links:* -
CAPER http://www.bprc.ac.cn/CAPE at Beijing Proteome Research Centerhttp://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-viewhttp://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:* -
Tutorialshttp://61.50.138.124/caper2/static/documentation/index.html -
Email: Dong Li lidong.bprc@foxmail.com, Dan Wangwangdanburnett@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/
This looks great.
I particularly like the modification of trackster to show MS/MS spectra ... that is very cool.
Some of the functions of CAPER look like they would be useful outside the C-HPP ... for different organisms for example. Is there any way we can install these features into a local galaxy?
Cheers Ira
On 6 Dec 2013, at 4:26 am, Dave Clements <clements@galaxyproject.orgmailto:clements@galaxyproject.org> wrote:
Hello all (proteomaticians?),
Please welcome a new public Galaxy server to the Galaxy proteomics community:
CAPERhttp://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/PublicGalaxyServers page 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
[CAPER]http://www.bprc.ac.cn/CAPE
* Links: * CAPERhttp://www.bprc.ac.cn/CAPE at Beijing Proteome Research Centerhttp://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 Projecthttp://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 Projecthttp://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-viewhttp://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: * Tutorialshttp://61.50.138.124/caper2/static/documentation/index.html * Email: Dong Limailto:lidong.bprc@foxmail.com, Dan Wangmailto:wangdanburnett@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/
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Thanks for your praise. Yes, we are trying to develop CAPER into an integrated knowledge discovery platform for -omics datasets, no only the C-HPP data. We are sorry that there is no package for CAPER to the local installation. And we are now considering to make one. Best, Dong Li
lidong 2013-12-06
发件人： Ira Cooke 发送时间： 2013-12-06 03:10:57 收件人： Dave Clements 抄送： Galaxy Proteomics List; Dong Li; Dan Wang 主题： Re: [galaxy-proteomics] CAPER: A new proteomics Galaxy Server
This looks great.
I particularly like the modification of trackster to show MS/MS spectra ... that is very cool.
Some of the functions of CAPER look like they would be useful outside the C-HPP ... for different organisms for example. Is there any way we can install these features into a local galaxy?
Cheers Ira
On 6 Dec 2013, at 4:26 am, Dave Clements clements@galaxyproject.org wrote:
Hello all (proteomaticians?),
Please welcome a new public Galaxy server to the Galaxy proteomics community:
CAPER: 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/PublicGalaxyServers page 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
Links: CAPER at Beijing Proteome Research Center, China "CAPER 2.0: An Interactive, Configurable, and Extensible Workflow-Based Platform to Analyze Data Sets from the Chromosome-centric Human Proteome Project" 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" 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, 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 Email: Dong Li, Dan Wang Quotas: Free for academic users. Creating an account is recommended. Sponsor(s): Beijing Proteome Research Center (BPRC), the Human Liver Proteome Project (HLPP), and the Chromosome-centric Human Proteome Project (C-HPP)
galaxy-proteomics@lists.galaxyproject.org
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Dave Clements -
Ira Cooke -
lidong