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workshop: June 2012

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Seb edited this page Jan 28, 2015 · 1 revision

BioJS workshop. EBI, 20 June, 2012

Attendees

We had some people at the EBI interested to learn more about BioJS, so we decided to organize a mini-workshop to show people how to use/develop BioJS components and get some feedback to improve the library. At the end we got 2 people from TGCA, 5 from the Sanger institute and 28 people from EBI.

  • Anil Thanki - TGCA
  • Xingdong Bian - TGCA
  • Eugene Bragin - Sanger
  • Dushyanth Jyothi - Sanger
  • Fabian Schreiber - Sanger
  • Frank Schwach - Sanger
  • Nick - Sanger
  • Leyla J Garcia- EBI
  • John Gomez- EBI
  • Rafael C Jimenez - EBI
  • Shaun - EBI
  • Antonio Fabregat - EBI
  • Mihai Glonț - EBI
  • Stathis Kanterakis - EBI
  • John May - EBI
  • Laurent Gil - EBI
  • Venkatesh Muthukrishnan - EBI
  • Swanand - EBI
  • Francis Rowland - EBI
  • Joseph Rossetto - EBI
  • Alan Da Silva - EBI
  • Mahmut Uludag - EBI
  • Peter Walter - EBI
  • Marine - EBI
  • Noemi del Toro - EBI
  • Rui Wang - EBI
  • Samuel Croset - EBI
  • Rodrigo Ochoa - EBI
  • Nicolas Rodriguez - EBI
  • Glen van Ginkel - EBI
  • Jonathan warren - EBI
  • Robert Petryszak - EBI
  • Vladimir Volynkin - EBI
  • Eduardo - EBI
  • Florian Reisinger - EBI

Agenda

  • 10:00 - 10:30, Introduction to the BioJS project
  • 10:30 - 11:00, How to use BioJS components and the registry
  • 11:00 - 12:00, Tutorial of how to develop a BioJS component
  • 12:00 - 13:00, Lunch break
  • 13:00 - 13:30, Brainstorming and short presentations of ideas
  • 13:30 - 17:00, Helping you to develop a BioJS component

Presentation

Feedback

  • To have a registry where people can show their interest to use or develop a component
  • To allow feedback and comments for components in the registry page
  • Check how to include unit testing for components
  • Add a FAQ secction. One general about BIoJS and other one per component
  • If available a component in the resgistry should hava a link to the requirements

Component ideas

Component ideas proposed to develop during or just after the workshop:

Plasmid representation

Represent plasmid annotations in a circular and linear way using an abstract representation. Proposed by Frank Schwach http://plasmogem.sanger.ac.uk/

Genome browser component

Create a component to representation of genome information using the latest development of the ENSEMBl canvas viewer. Proposed by Eugene Bragin

Periodic table

A table of the chemical elements as a exercise to learn how to develop a BioJS Proposed by Glen van Ginkel http://www.ptable.com/

Ontology visualization

Graph view of ontology terms. Proposed by Venkatesh Muthukrishnan http://www.ebi.ac.uk/chebi/chebiOntology.do?chebiId=CHEBI:35135

Tissue expression images

A component to visualize tissue expression images Proposed by Jonathan warren

Features for 3D structures

Display UniProt? coverage, all the PDB acceccion for a UniProt? accession. Proposed by Swanard http://www.ebi.ac.uk/pdbe-apps/widgets/unipdb?uniprot=P60493

3D structure image slideshow

A component to visualize protein structure images for one PDB acc Proposed by Swanard http://www.ebi.ac.uk/pdbe-srv/view/entry/3sip/summary

PDBe legend image

Legend to describe information available for one specific PDB accession Proposed by Swanard http://www.ebi.ac.uk/pdbe-srv/view/entry/3sip/summary

Display PDB structures for UniProt? accession

Improve to current Protein3DUniprot component to collect information from the PDBe webservide instead of the DAS alignment server. Sort structures by confidence score suing the new service of PDBe. Developed by John. Swanard willing to accept this feature request. http://www.ebi.ac.uk/~jgomez/biojs/registry/Biojs.Protein3DUniprot.html

ChEMBL component with hig resolution images

Modify or extend the ChEMBL component to include high resolution images like the ChEBI component. Developed by John. Shaun willing to accept this feature request. http://www.ebi.ac.uk/~jgomez/biojs/registry/Biojs.ChEMBLCompound.html

Improve interaction table

This table is taking as input molecular interactions in PSI-MITAB, however it is not parsing well. Developed by John. Rafael willing to accept this feature request. http://www.ebi.ac.uk/~jgomez/biojs/registry/Biojs.InteractionsTable.html

Interaction table integrating intereaction from several PSICQUIC resources

Component extending the interaction table to query several PSIQUIC services with a MIQL query. Proposed by Marine http://www.ebi.ac.uk/~jgomez/biojs/registry/Biojs.InteractionsTable.html

Phylogenetic trees

Create a BioJS component for phylogenetic trees based on the TreeFam? project Proposed by Fabian Schreiber

Phylogenetic trees

Create a BioJS component for phylogenetic trees based on Ian Sillitoe's project Proposed by Ian Sillitoe (UCL)

Sequence alignments

Create a BioJS component for sequence alignments based on the TreeFam? project Proposed by Fabian Schreiber

Sequence alignments

Create a BioJS component for sequence alignments based on Ian Sillitoe's project Proposed by Ian Sillitoe (UCL)

Structural viewer

Create a BioJS component for structural views based on Ian Sillitoe's project Proposed by Ian Sillitoe (UCL)

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