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andrewrobertjones edited this page Sep 18, 2017 · 39 revisions

Bioinformatics Hub at the HUPO 2017 World Congress

Overview

The Bioinformatics Hub is a place where bioinformaticians gather together with three aims: (i) to provide their advice, knowledge, and support to anyone with a relevant question; (ii) to discuss current issues and challenges in proteomics informatics with the entire community; and (iii) to work on interesting, synergistic projects and to freely exchange tools, algorithms and know-how with each other, across all labs, seniorities and levels of experience.

This is achieved by specific sessions in the agenda. The Ask the Experts sessions (every day between 11h30 and 12h30) explicitly open the floor to anyone with a question, and leverages the combined experience and expertise of all Hub participants to answer those questions. The Special Interest Topic sessions address a current problem or issue in proteomics informatics in a short (max 20 min lecture), followed by an open, discussion of the topic by all participants, moderated by the organizers. The last type of session, the workshop style sessions, allow participants to work on synergistic topics of their choice, or to exchange know-how, tools and algorithms with the other participants.

The Bioinformatics Hub operates under an open door policy, and that anyone is free to walk in at any time and participate in the work or the discussions, ask a question of someone, or just listen in on what is going on! The bioinformatics hub is meant to be inclusive, low threshold, and aimed at knowledge exchange across all levels of experience.

Also note that representatives from the vendors are very much welcome to participate in the Hub, and typically are well-represented indeed. So your questions on vendor software can also be handled by the experts!

Hashtags for Twitter

#BioinformaticsHub #HUPO2017

Main Congress

Bioinformatics Hub Schedule:

Sunday September 17:

On Sunday only, the Bioinformatics Hub will be located at the O’Brien Centre for Science on the University College Dublin Campus. This is the same location as the HPP Workshop and Mentoring Day activities. See map for details. The Hub will be in Room ALE H2.38.

  • 08h30-09h00: Arrival
  • 09h00-9h30: Introduction and concept by organizers (Andy Jones et al.)
  • 9h30-10h00: Stand-up introductions
  • 10h00-13h00: Pitches: up to 15 minutes for anyone who wants to propose a topic to work on, for instance:
    • a tool, library or approach that could be useful for someone
    • a problem they want address (during the meeting) and can use some help on
    • a currently neglected question that they think is important to the field
    • a tool that is currently missing and which they possibly would like to (help) develop
  • 13h00-14h00: Lunch break. Sack lunch provided.
  • 14h00-15h00: Pitches [continued] - Continued 15 minute pitches. These pitches are meant to create seed cores around which people can organize for the subsequent days' workshop sessions
  • 15h00-16h45: Split up into smaller groups and proceed workshop style
  • 17h00-17h00: Coaches depart UCD for Convention Centre

Monday September 18:

For Monday through Wednesday, the Bioinformatics Hub will be held in a special area in the main Exhibition and Sponsor Area (the Forum) on the ground floor of the Convention Centre (CCD).

Note: in a change to the published scheduled, morning sessions will start at 9.50am to avoid clashes with the plenary session

Tuesday September 19:

  • 09h50-11h30: Special Interest Topic: Immuno-peptidomics (Pouya Faridi)
  • 11h30-12h30: Ask the Experts sessions
  • 12h30-13h30: Lunch break
  • 13h30-15h30: Special Interest Topic: Confidence in PTM identification (Andy Jones)
  • 15h30-17h30: Special Interest Topic: Universal spectrum identifier (Eric Deutsch)

Wednesday September 20:

Confirmed Pitches:

  • Real-time proteomics: expectations, issues and solutions (David Bouyssié)
  • In Immunopeptidomics we need a sniper instead of a shotgun (Pouya Faridi)
  • Use published data/or measured datasets per organism to do proteogenomics, and direct input to UniProt (Stephan Michalik)
  • Sound uses for entrapment sequence datasets (Andrew Dowsey)
  • Preprocessing by spectral clustering (Johannes Griss)
  • qcML and cloud-based proteomics processing (Mathias Walzer)
  • Re-use published data for your research (Johannes Griss)
  • How good should our evidence be that we have seen a PTM via mass spec? (Andy Jones)

Other possible pitches

  • Achieving universal implementation of data standards (Andy Jones)
  • Can we build large-scale co-expression networks from quantitative proteomics data (Andy Jones)
  • HPP Data Interpretation Guidelines (Eric Deutsch)
  • MissingProteinPedia (Mohammad T Islam)
  • Use of bioRXiv in Computational Proteomics (Eric Deutsch)
  • JPR Annual Special Issue on Proteomics Informatics Tools (TBC)
  • Statistical testing in proteomics (Lieven Clement & Veit Schwämmle)
  • Re-use published data for your research (TBD)
  • The Universal Spectrum Identifier (Eric Deutsch)
  • Gathering evidence for translation of lncRNAs (Eric Deutsch)
  • How to agree that a protein is too hard to acquire by MS (Eric Deutsch)

Attending Organizers:

  • Lennart Martens
  • Juan Antonio Vizcaíno
  • Eric Deutsch
  • Andy Jones
  • Nuno Bandeira
  • Henning Hermjakob
  • Yasset Perez-Riverol
  • Yves Vandenbrouck
  • EuBIC (proteomics-academy.org)

Other Confirmed Participants

  • All others are welcome!

Special Planned Topics:

TBD

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