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Bio

gmod.org is DOWN, 1618265286

GMOD.org status - Mon, 04/12/2021 - 18:44
Categories: Bio

AGR GFF

AGR GFF uploads - Thu, 04/08/2021 - 18:36
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File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":43,"name":"HUMAN","description":"Human"},"stableURL":"https://fms.alliancegenome.org/download/GFF_HUMAN.gff.gz","s3Url":"https://download.alliancegenome.org/4.0.0/GFF/HUMAN/GFF_HUMAN_2.gff.gz"},{"id":61000,"s3Path":"3.2.0/GFF/ZFIN/GFF_ZFIN_2.gff","md5Sum":"96158209680d20f631fe6525b5716af7","valid":true,"uploadDate":"2020-09-02T14:36:14.278+0000","releaseVersions":[{"id":66180,"releaseVersion":"4.0.0","releaseDate":"2021-03-23T04:00:00.000+0000"},{"id":88275,"releaseVersion":"4.1.0","releaseDate":"2021-06-23T04:00:00.000+0000"},{"id":15546,"releaseVersion":"3.2.0","releaseDate":"2020-10-19T00:00:00.000+0000"}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":46,"name":"ZFIN","description":"Zebrafish Information Network"},"stableURL":"https://fms.alliancegenome.org/download/GFF_ZFIN.gff","s3Url":"https://download.alliancegenome.org/3.2.0/GFF/ZFIN/GFF_ZFIN_2.gff"},{"id":85610,"s3Path":"3.2.0/GFF/SGD/GFF_SGD_4.gff.gz","md5Sum":"ab40b0bf112401e6533463f6b0e87b58","valid":true,"uploadDate":"2021-01-27T02:24:17.383+0000","releaseVersions":[{"id":66180,"releaseVersion":"4.0.0","releaseDate":"2021-03-23T04:00:00.000+0000"},{"id":88275,"releaseVersion":"4.1.0","releaseDate":"2021-06-23T04:00:00.000+0000"},{"id":15546,"releaseVersion":"3.2.0","releaseDate":"2020-10-19T00:00:00.000+0000"}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":48,"name":"SGD","description":"Saccharomyces Genome Database"},"stableURL":"https://fms.alliancegenome.org/download/GFF_SGD.gff.gz","s3Url":"https://download.alliancegenome.org/3.2.0/GFF/SGD/GFF_SGD_4.gff.gz"}]
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Thu, 04/01/2021 - 14:58

‎Creating learning paths within the Galaxy Training Network: Updated pub.

← Older revision Revision as of 18:58, 1 April 2021 (4 intermediate revisions by the same user not shown)Line 129: Line 129:  *''Expected results:'' Datatype format and semantics help would be widely available when using Galaxy, including in tools that consume and produce particular datatypes, as well as server-wide help describing supported datatypes. *''Expected results:'' Datatype format and semantics help would be widely available when using Galaxy, including in tools that consume and produce particular datatypes, as well as server-wide help describing supported datatypes.  *''Project Home Page URL:'' https://galaxyproject.org/ *''Project Home Page URL:'' https://galaxyproject.org/ −*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434+*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. ''Nucleic Acids Research'', 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  *''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end. *''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  *''Skill level:'' Basic *''Skill level:'' Basic Line 139: Line 139:  *''Expected results:'' Users will know immediately what a server's quotas are, and what items are contributing most to consuming their quota.  Users will have a clear idea of what they can expect, and what they can do to increase their available resources. *''Expected results:'' Users will know immediately what a server's quotas are, and what items are contributing most to consuming their quota.  Users will have a clear idea of what they can expect, and what they can do to increase their available resources.  *''Project Home Page URL:'' https://galaxyproject.org/ *''Project Home Page URL:'' https://galaxyproject.org/ −*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434+*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. ''Nucleic Acids Research'', 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  *''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end. *''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  *''Skill level:'' Medium *''Skill level:'' Medium  *''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global. *''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global.  +  +== Creating learning paths within the Galaxy Training Network ==  +  +*''Brief explanation:'' Implement and display learning paths in the Galaxy Training Material infrastructure to show learners, especially newcomers, which tutorial they should take first or which sequence of tutorials to follow to become knowledgeable about a particular topic.  +*''Expected results:'' An easy way to configure and update learning paths. Easy to understand and navigate learning paths for web site users.  +*''Project Home Page URL:'' https://training.galaxyproject.org/  +*''Project paper reference and URL:'' Batut, B., Hiltemann, S., Bagnacani, A., Baker, D., Bhardwaj, V., Blank, C., Bretaudeau, A., Brillet-Guéguen, L., Čech, M., Chilton, J., Clements, D., Doppelt-Azeroual, O., Erxleben, A., Freeberg, M. A., Gladman, S., Hoogstrate, Y., Hotz, H.-R., Houwaart, T., Jagtap, P., … Grüning, B. (2018). Community-Driven Data Analysis Training for Biology. ''Cell Systems'', 6(6), 752-758.e1. https://doi.org/10.1016/j.cels.2018.05.012  +  +*''Knowledge prerequisites:''  Ruby, JavaScript (some Python).  +*''Skill level:'' Medium  +*''Mentors:'' Bérénice Batut, University of Freiburg (berenice DOT batut[at] gmail.com).  Galaxy Outreach & Training Working Group, global.     == Template: Project Idea Name (Project Name/Lab Name) == == Template: Project Idea Name (Project Name/Lab Name) == Clements
Categories: Bio

File:Minimize button demo.gif

GMOD.org recent changes - Tue, 03/30/2021 - 14:51
Categories: Bio

File:Upstream downstream.png

GMOD.org recent changes - Tue, 03/30/2021 - 14:45
Categories: Bio

Main Page

GMOD.org recent changes - Tue, 03/30/2021 - 14:22

‎Popular GMOD Tools

← Older revision Revision as of 18:22, 30 March 2021 Line 44: Line 44:     <div class="logos"> <div class="logos">  +[[File:Jbrowse2_logo.png|250px|thumb|none|link=JBrowse|JBrowse 2: New super-fast genome annotation viewer]]  [[File:GBrowseLogo.png|250px|thumb|none|link=GBrowse|GBrowse: Genome annotation viewer]] [[File:GBrowseLogo.png|250px|thumb|none|link=GBrowse|GBrowse: Genome annotation viewer]]  [[File:GalaxyLogoBigger.png|250px|thumb|none|link=Galaxy|Galaxy: Data analysis & integration]] [[File:GalaxyLogoBigger.png|250px|thumb|none|link=Galaxy|Galaxy: Data analysis & integration]] Scott
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Mon, 03/29/2021 - 10:26

‎Interactive viewer for systems-biology variant interpretation (Server-side)

← Older revision Revision as of 14:26, 29 March 2021 (One intermediate revision by the same user not shown)Line 26: Line 26:  **''Knowledge prerequisites:'' JavaScript **''Knowledge prerequisites:'' JavaScript  **''Skill level:'' Medium **''Skill level:'' Medium −**''Mentors:'' Shraddha Pai  +**''Mentors:'' Shraddha Pai − +** [https://docs.google.com/document/d/1XhFAUVUeWV98PQcBMhjpH8HCpdQ15YbsrCNE5Rir1eM/edit Project Description]  +   == Interactive viewer for systems-biology variant interpretation (Server-side)==   == Interactive viewer for systems-biology variant interpretation (Server-side)==    **''Brief explanation:'' Create server-side database and application for system-level annotation of variants/gene, to connect to interactive UI (e.g. selected single-cell marker datasets , known disease associations, drug targets).   **''Brief explanation:'' Create server-side database and application for system-level annotation of variants/gene, to connect to interactive UI (e.g. selected single-cell marker datasets , known disease associations, drug targets).   Line 35: Line 36:  **''Skill level:'' Medium **''Skill level:'' Medium  **''Mentors:'' Shraddha Pai **''Mentors:'' Shraddha Pai  +** [https://docs.google.com/document/d/1XhFAUVUeWV98PQcBMhjpH8HCpdQ15YbsrCNE5Rir1eM/edit Project Description]     == Style Guides for Biological Information Portal (WormBase / Alliance of Genome Resources)==   == Style Guides for Biological Information Portal (WormBase / Alliance of Genome Resources)==   Shraddhapai
Categories: Bio

gmod.org is DOWN, 1616393281

GMOD.org status - Mon, 03/22/2021 - 02:36
Categories: Bio

gmod.org is DOWN, 1616386081

GMOD.org status - Mon, 03/22/2021 - 00:36
Categories: Bio

gmod.org is DOWN, 1616378881

GMOD.org status - Sun, 03/21/2021 - 22:36
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Tue, 03/16/2021 - 22:04

← Older revision Revision as of 02:04, 17 March 2021 Line 59: Line 59:  **''Project Home Page URL:'' https://www.alliancegenome.org/. **''Project Home Page URL:'' https://www.alliancegenome.org/.  **''Project paper reference and URL:'' [https://pubmed.ncbi.nlm.nih.gov/31796553/ The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases] **''Project paper reference and URL:'' [https://pubmed.ncbi.nlm.nih.gov/31796553/ The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases] −**''Knowledge prerequisites:'' Python, Microservices.+**''Knowledge prerequisites:'' Python, JavaScript, Microservices.  **''Skill level:'' Medium. **''Skill level:'' Medium.  **''Mentors:'' Adam Wright (adam.wright@wormbase.org). **''Mentors:'' Adam Wright (adam.wright@wormbase.org). Awright
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Mon, 03/15/2021 - 17:46

‎Bioinformatics Resource - Data Pipeline for Systematic Feature Extraction of Major Single-Cell Resources Utilizable for Downstream Analysis (Reactome)

← Older revision Revision as of 21:46, 15 March 2021 (2 intermediate revisions by the same user not shown)Line 107: Line 107:     ==Bioinformatics Resource - Data Pipeline for Systematic Feature Extraction of Major Single-Cell Resources Utilizable for Downstream Analysis (Reactome)== ==Bioinformatics Resource - Data Pipeline for Systematic Feature Extraction of Major Single-Cell Resources Utilizable for Downstream Analysis (Reactome)== −*''Brief explanation:'' Build a dockized systematic data pipeline that modulates feature extraction of 3 major single-cell data resource. Demonstrate EDA, quality of data and feature extraction workflow in Jupyter Notebook.   +*''Brief explanation:'' Build a dockized systematic data pipeline that modulates feature extraction of single cell data in both human and mice tissues. For this project, we will focus on Descartes data resource [https://descartes.brotmanbaty.org/] with 121 human and 61 mice organogenesis tissues. This data resource has gone through preprocessing steps utilizing monocle3 [https://cole-trapnell-lab.github.io/monocle3/]. For feature extraction, we will leverage Reactomes' curated data and utilize libraries such as scanpy [https://scanpy.readthedocs.io/en/stable/index.html], scVelo [https://scvelo.readthedocs.io/], pySCENIC [https://pyscenic.readthedocs.io/en/latest/index.html], and ssGSEA. All steps including EDA, quality of data, feature extraction, and pathway activity workflow will be demonstrated in Jupyter Notebook.    −*''Expected results:'' Dockerized python3 client with automated pipeline that gathers Single-Cell features and saves results in AnnData per each tissue or disease type. The resource is utilizable for downstream pathway or network based analysis in bioinformatics community with validated pathway activity in each type. A jupyter notebook demonstrating pipeline and quality of data.+*''Expected results:'' Dockerized python3 client with automated pipeline that gathers and processes Single-Cell features in each tissue type. The resource is utilizable for downstream pathway or network based analysis in bioinformatics community with validated pathway activity in each type. A jupyter notebook demonstrating feature extraction pipeline and pathway activity.  * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. * ''Project Home Page URL:'' [https://reactome.org. reactome.org]. −* ''Knowledge prerequisites:'' Python3, Single-Cell Bioinformatics Objects & Feature Extraction Processes, Dockers, MongoDB (not-required) +* ''Knowledge prerequisites:'' Python3, Single-Cell Bioinformatics Processes, Feature Extraction, Dockers  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Nasim Sanati (sanati[AT]ohsu.edu or nasim[AT]plenary.org) Solomon Shorser (solomon.shorser[AT]oicr.on.ca) * ''Mentors:'' Nasim Sanati (sanati[AT]ohsu.edu or nasim[AT]plenary.org) Solomon Shorser (solomon.shorser[AT]oicr.on.ca) Nasim
Categories: Bio

gmod.org is DOWN, 1615442881

GMOD.org status - Thu, 03/11/2021 - 01:09
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Mon, 03/08/2021 - 13:20

← Older revision Revision as of 18:20, 8 March 2021 (2 intermediate revisions by the same user not shown)Line 97: Line 97:  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca)  +  +==Bioinformatics Visualization Library - Mapping Reactome Pathway Hierarchy to Low Dimension Manifolds (Reactome)==  +*''Brief explanation:'' Build an interactive and dynamic D3 or webGL based dimention reduction visualization library with the ability to tinker Reactome Pathway Hierarchy Network features. Demonstrate usability and features in Jupyter Notebook.   +*''Expected results:'' A bundled javascript visualization library of tSNE, UMAP, and PCA plots designed for python programmers in bioinformatics community with a focus on Reactome Pathway Hierarchy features. Jupyter Notebook demonstrating usability and features.  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Python3, D3 or webGL, javascript  +* ''Skill level:'' Medium.  +* ''Mentors:'' Nasim Sanati (sanati[AT]ohsu.edu or nasim[AT]plenary.org) Solomon Shorser (solomon.shorser[AT]oicr.on.ca)  +  +==Bioinformatics Resource - Data Pipeline for Systematic Feature Extraction of Major Single-Cell Resources Utilizable for Downstream Analysis (Reactome)==  +*''Brief explanation:'' Build a dockized systematic data pipeline that modulates feature extraction of 3 major single-cell data resource. Demonstrate EDA, quality of data and feature extraction workflow in Jupyter Notebook.   +*''Expected results:'' Dockerized python3 client with automated pipeline that gathers Single-Cell features and saves results in AnnData per each tissue or disease type. The resource is utilizable for downstream pathway or network based analysis in bioinformatics community with validated pathway activity in each type. A jupyter notebook demonstrating pipeline and quality of data.  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Python3, Single-Cell Bioinformatics Objects & Feature Extraction Processes, Dockers, MongoDB (not-required)  +* ''Skill level:'' Medium.  +* ''Mentors:'' Nasim Sanati (sanati[AT]ohsu.edu or nasim[AT]plenary.org) Solomon Shorser (solomon.shorser[AT]oicr.on.ca)  +  +==Bioinformatics Data Science - Reactome Pathway Embeddings (Reactome)==  +*''Brief explanation:'' Utilize established methods and simulated data to find pathway embeddings in human Reactome pathway hierarchy graph. These pathway representations may be used in downstream analysis as biological processes features that are involved/not-involved within disease or other biological context.  +*''Expected results:'' Python client with the capability to compute graph embeddings of human Reactome pathway hierarchy within different context and compare the differences and/or similarities between embeddings results with validated examples.  +* ''Project Home Page URL:'' [https://reactome.org. reactome.org].  +* ''Knowledge prerequisites:'' Python3, Keras/Tensorflow, Machine Learning & Feature Extraction, Biological Networks  +* ''Skill level:'' Medium/Advanced.  +* ''Mentors:'' Nasim Sanati (sanati[AT]ohsu.edu or nasim[AT]plenary.org)     == Datatypes Help in Galaxy (Galaxy) == == Datatypes Help in Galaxy (Galaxy) == Nasim
Categories: Bio

User:Nasim

GMOD.org recent changes - Mon, 03/08/2021 - 12:48

User account Nasim was created by Scott

Scott
Categories: Bio

User:Nasim

GMOD.org recent changes - Mon, 03/08/2021 - 12:48

Creating user page for new user.

New page

Computational Biologist with experience in data engineering, analytics, and science. Achievements include designing and building agile pipelines, measuring and defining existing data schemas for enhancement of feature extraction performance, and building models that best fit innovative problems within clinical or molecular context. Proven ability in demonstrating results to an interdisciplinary audience of MD’s, scientists, engineers, and research associates. Successfully led and timely delivered multiple projects, working independently and on collaborative teams. Passionate in bridging the gap between clinical research implementation and clinical utility by identifying molecular abnormalities to advance early detection, prognosis, and risk stratification. Dedicated to collaborative open access science and innovation. Scott
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Wed, 03/03/2021 - 12:07

‎Create a workflow directory for Galaxy Community (Galaxy): Dropped proposal. IWC in Galaxy is working on this.

← Older revision Revision as of 17:07, 3 March 2021 Line 117: Line 117:  *''Skill level:'' Medium *''Skill level:'' Medium  *''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global. *''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global. −  −== Create a workflow directory for Galaxy Community (Galaxy) ==  −  −*''Brief explanation:'' Publicly available Galaxy workflows are distributed across many types of websites: WorkflowHub, Dockstore, and MyExperiment; Galaxy Tool Shed; Zenodo; and public Galaxy servers.  Create a united site that researchers can use to find these workflows.  −*''Expected results:'' Users can easily locate shared Galaxy workflows, no matter where they are. The web site admins can easily define and add new workflow sources.   −*''Project Home Page URL:'' https://galaxyproject.org/  −*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  −*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  −*''Skill level:'' Medium  −*''Mentors:'' Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org)      == Template: Project Idea Name (Project Name/Lab Name) == == Template: Project Idea Name (Project Name/Lab Name) == Clements
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Wed, 03/03/2021 - 12:07

‎Create a workflow directory for Galaxy Community (Galaxy): Dropped proposal. IWC in Galaxy is working on this.

← Older revision Revision as of 17:07, 3 March 2021 (One intermediate revision by the same user not shown)(No difference) Clements
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Wed, 03/03/2021 - 12:07

‎Create a workflow directory for Galaxy Community (Galaxy): Dropped proposal. IWC in Galaxy is working on this.

← Older revision Revision as of 17:07, 3 March 2021 (5 intermediate revisions by the same user not shown)Line 97: Line 97:  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca)  +  +== Datatypes Help in Galaxy (Galaxy) ==  +  +*''Brief explanation:'' Create infrastructure for providing datatype help in Galaxy.  Includes expanding datatype definitions and updating Galaxy user interface to take advantage of it.  +*''Expected results:'' Datatype format and semantics help would be widely available when using Galaxy, including in tools that consume and produce particular datatypes, as well as server-wide help describing supported datatypes.  +*''Project Home Page URL:'' https://galaxyproject.org/  +*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  +*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  +*''Skill level:'' Basic  +*''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global.  +  +== Provide users with better quota information (Galaxy) ==  +  +*''Brief explanation:'' Publish each server's quotas in a standard way; provide users with more information about what analyses and datasets are consuming their quota allocation.  +*''Expected results:'' Users will know immediately what a server's quotas are, and what items are contributing most to consuming their quota.  Users will have a clear idea of what they can expect, and what they can do to increase their available resources.  +*''Project Home Page URL:'' https://galaxyproject.org/  +*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  +*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  +*''Skill level:'' Medium  +*''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global.     == Template: Project Idea Name (Project Name/Lab Name) == == Template: Project Idea Name (Project Name/Lab Name) == Clements
Categories: Bio

GSOC Project Ideas 2021

GMOD.org recent changes - Tue, 03/02/2021 - 16:48

‎Create a workflow directory for Galaxy Community (Galaxy): Added this section

← Older revision Revision as of 21:48, 2 March 2021 (4 intermediate revisions by the same user not shown)Line 97: Line 97:  * ''Skill level:'' Medium. * ''Skill level:'' Medium.  * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca) * ''Mentors:'' Robin Haw (robin.haw[AT]oicr.on.ca) Solomon Shorser (solomon.shorser[AT]oicr.on.ca)  +  +== Datatypes Help in Galaxy (Galaxy) ==  +  +*''Brief explanation:'' Create infrastructure for providing datatype help in Galaxy.  Includes expanding datatype definitions and updating Galaxy user interface to take advantage of it.  +*''Expected results:'' Datatype format and semantics help would be widely available when using Galaxy, including in tools that consume and produce particular datatypes, as well as server-wide help describing supported datatypes.  +*''Project Home Page URL:'' https://galaxyproject.org/  +*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  +*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  +*''Skill level:'' Basic  +*''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global.  +  +== Provide users with better quota information (Galaxy) ==  +  +*''Brief explanation:'' Publish each server's quotas in a standard way; provide users with more information about what analyses and datasets are consuming their quota allocation.  +*''Expected results:'' Users will know immediately what a server's quotas are, and what items are contributing most to consuming their quota.  Users will have a clear idea of what they can expect, and what they can do to increase their available resources.  +*''Project Home Page URL:'' https://galaxyproject.org/  +*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  +*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  +*''Skill level:'' Medium  +*''Mentors:'' Björn Grüning, University of Freiburg (bjoern.gruening[at]gmail.com); Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org); Galaxy Support Working Group, global.  +  +== Create a workflow directory for Galaxy Community (Galaxy) ==  +  +*''Brief explanation:'' Publicly available Galaxy workflows are distributed across many types of websites: WorkflowHub, Dockstore, and MyExperiment; Galaxy Tool Shed; Zenodo; and public Galaxy servers.  Create a united site that researchers can use to find these workflows.  +*''Expected results:'' Users can easily locate shared Galaxy workflows, no matter where they are. The web site admins can easily define and add new workflow sources.  +*''Project Home Page URL:'' https://galaxyproject.org/  +*''Project paper reference and URL:'' Jalili, V., Afgan, E., Gu, Q., Clements, D., Blankenberg, D., Goecks, J., Taylor, J., & Nekrutenko, A. (2020). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research, 48(W1), W395–W402. https://doi.org/10.1093/nar/gkaa434  +*''Knowledge prerequisites:''  Python and JavaScript.  Will use Vue.js components in front end.  +*''Skill level:'' Medium  +*''Mentors:'' Dave Clements, Johns Hopkins University (clements[at]galaxyproject.org)     == Template: Project Idea Name (Project Name/Lab Name) == == Template: Project Idea Name (Project Name/Lab Name) == Clements
Categories: Bio

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