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Eric Deutsch edited this page Oct 18, 2016 · 50 revisions

Bioinformatics Hub at the HUPO 2016 World Congress

This event has concluded successfully. We thank the many participants to came to the hub. The agenda and related information about the hub is still posted below for follow-on work. Planning is underway to prepare for another Bioinformatics Hub next year at the 2017 World Congress.

Hashtags for Twitter

#HUPO2016 #BioInformaticsHub

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 9h30 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!

Schedule (Note: event has now concluded):

Sunday September 18:

  • 08h30-09h00: Arrival
  • 09h00-9h30: Introduction and concept by organizers (Lennart Martens et al.)
  • 9h30-10h00: Stand-up introductions
  • 10h00-12h00: 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
  • 12h00-13h00: Lunch break
  • 13h00-15h00: 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
  • 15h00-17h30: Split up into smaller groups and proceed workshop style
    • Juanan, lnnrt: Bioinformatics Hub manuscript

Monday September 19:

  • 09h30-11h30: Special Interest Topics
  • 11h30-12h30: Ask the Experts sessions
  • 12h30-13h30: Lunch break
  • 13h30-15h30: Hub moves to the Bioinformatics Session of HUPO - Room: 101 AB, 1F
  • 15h30-17h30:
    • Publication of proteomics software tools
      • JPR Annual Special Issue on Proteomics Informatics Tools (lnnrt & Sue Weintraub)
      • Use of bioRXiv in Computational Proteomics & relation to Open Access (Eric Deutsch)

Tuesday September 20:

  • 09h30-11h30: Special Interest Topics
    • Data interpretation
      • HPP Data Interpretation Guidelines (Eric Deutsch)
    • 'Missing' proteins and tricky identifications
      • MissingProteinPedia (Mohammad T Islam, Charlie Ahn, Abidali Mohamedali, Mark Baker)
      • neXt 50 Missing Protein Chase (Chris Overall)
  • 11h30-12h30: Ask the Experts sessions
  • 12h30-13h30: Lunch break
  • 13h30-15h30: Workshop style sessions
  • 15h30-17h30: Special Interest Session (continued from previous Protein Standards session, Room: 102, 1F)
    • Standards and formats
      • Collaborating with the newly formed PSI-QC workgroup for better QC (Mathias Walzer)
      • Proteogenomics data formats (Juan Antonio Vizcaíno)
      • **RESCHEDULED: **FDR: On the difference between filtering false discoveries and estimating their proportion (Thomas Burger)

Wednesday September 21:

  • 09h30-10h30: Workshop style sessions
  • 10h30-12h30: Glycoproteomics Informatics (details below)
  • 12h30-13h30: Lunch break
  • 13h30-15h30: Special interest topic + discussion
  • 13h30-15h30: Glycoproteomics Informatics Ask the Experts session
  • 15h30-17h30: continue workshop style session

Pitches:

  • Data interpretation
    • HPP Data Interpretation Guidelines (Eric Deutsch)
    • FDR: On the difference between filtering false discoveries and estimating their proportion (Thomas Burger)
  • 'Missing' proteins and tricky identifications
    • MissingProteinPedia (Mohammad T Islam, Charlie Ahn, Abidali Mohamedali, Mark Baker)
    • neXt 50 Missing Protein Chase (Chris Overall)
    • Glycoproteomics Informatics (Kay-Hooi Khoo)
  • Public data
    • Privacy and proteomics data (Henning Hermjakob)
    • OmicsDI: finding the right dataset (Yasset Perez-Riverol)
    • PRIDE Cluster: Big Data and Proteomics (Juan Antonio Vizcaíno)
  • Standards and formats
    • Collaborating with the newly formed PSI-QC workgroup for better QC (Mathias Walzer)
    • Proteogenomics data formats (Juan Antonio Vizcaíno)
  • Tools and frameworks
    • BioDocker (Yasset Perez-Riverol)
    • OpenMS 2.0: a flexible open-source software platform for mass spectrometry data analysis(Mathias Walzer)
  • Publication of proteomics software tools
    • Use of bioRXiv in Computational Proteomics (Eric Deutsch)
    • JPR Annual Special Issue on Proteomics Informatics Tools (lnnrt & Sue Weintraub)
    • Open access fees (Henning Hermjakob)

Attending Organizers:

  • Lennart Martens
  • Juan Antonio Vizcaíno
  • Eric Deutsch
  • Nuno Bandeira
  • Henning Hermjakob
  • Yasset Perez-Riverol
  • Mathias Walzer
  • Yves Vandenbrouck
  • Henry Lam

Other Confirmed Participants

  • Hannes Röst
  • Kay-Hooi Khoo
  • Mohammad Islam
  • Chris Overall
  • Thomas Burger
  • George Rosenberger
  • Hendrik Weisser
  • All others are welcome!

Special Planned Topics:

Glycoproteomics Informatics (Organizer: Kay-Hooi Khoo)

  • Wednesday 10h30-12h30: Special Interest Topic: Glycoproteomics Informatics
    • This 2h Special Interest Topic session will comprise several 20-30 min talks/tutorials on the use of Prospector, Byonic, Pinnacle and other computational tools developed by academic labs for glycoproteomics MS/MS data mining. It aims to provide insider tips and to address some of the pitfalls and FDR issues.
  • Wednesday 13h30-15h30: Glycoproteomics Informatics: Ask the Experts/Workshop Session - Will be organized based on the interests generated and received prior to and during the above Special Topics Session. - For all updates and further information, please visit http://glycosolutions.weebly.com/

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