HUPO 2018

Eric Deutsch edited this page Oct 1, 2018 · 26 revisions

Bioinformatics Hub at the HUPO 2018 World Congress


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 16h00 and 17h00) explicitly open the space to all with questions, 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) presentation, 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.

Hashtags for Twitter

#BioinformaticsHub #HUPO2018

Main Congress

Bioinformatics Hub Schedule:

Sunday September 30:

  • 08h30-09h00: Arrival
  • 09h00-9h30: Introduction and concept by organizers and stand-up introductions (Juan Antonio Vizcaíno et al.)
  • 9h30-12h00: 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.
  • 13h00-17h45: Split up into smaller groups and proceed workshop style

Monday October 1:

  • 09h15-09h30: Arrival
  • 09h30-10h30: Special Interest Topic #1 - Analyzing the HPP MS Pillar 96-phosphopeptides standard assay results (Ulrike Kusebauch, Magnus Palmblad, Michael Hoopmann, Susan Weintraub)
  • 10h30-11h30: Special Interest Topic #2a - free
  • 11h30-12h30: Special Interest Topic #2b - Computational predictions for uPE1 protein functional annotation with I-TASSER and COFACTOR (Gil Omenn, Hongjiu Zhang, Chengxin Zhang)
  • 12h30-12h45: Lunch break
  • 12h45-13h45: Special Interest Topic #3 - free
  • 14h00-16h00: Special Interest Topic #4 - PSI/ProteomeXchange session
    • 2:00 Standards of the HUPO Proteomics Standards Initiative (Eric Deutsch)
    • 2:30 PSI Molecular Interactions and IMEx (Sandra Orchard)
    • 2:45 Status and new features in UniProtKB (Sandra Orchard)
    • 3:00 Progress in developing a Universal Spectrum Identifier, PSI spectral library format, and PROXI API (Eric Deutsch)
    • 3:20 Status and new developments in the ProteomeXchange Consortium (Juan Antonio Vizcaíno)
    • 3:50 Open Discussion (all)
  • 16h00-17h00: Ask the Experts session

Tuesday October 2:

  • 09h15-09h30: Arrival
  • 09h30-10h30: Special Interest Topic #5 - "It is time to go Bayesian on Proteomics" (Lukas Käll)
  • 10h30-11h20: Special Interest Topic #6a - “Stranded peptides” in silico approach to finding PE2-4 Missing Proteins combined with SRM Atlas spectral matches to validate missing proteins (Tadashi Yamamoto)
  • 11h20-12h20: Special Interest Topic #6b -
  • 12h20-12h45: Lunch break
  • 12h45-13h45: Special Interest Topic #7 - Bioinformatics Guidance for Use of Popular Proteins Research (Kun-Hsing Yu, Maggie Lam, Edward Lau, Jenny van Eyk)
  • 14h00-15h50: Special Interest Topic #8a - Unscheduled time (Parallel computational session TOB)
  • 15h50-16h10: Special Interest Topic #8b - Spectral Libraries for DIA
  • 16h00-17h00: Ask the Experts session

Wednesday October 3:

  • 09h15-09h30: Arrival
  • 09h30-10h30: Special Interest Topic #9 - Protein Exceptions to the HPP Guidelines (Eric Deutsch, Lydie Lane, Gil Omenn)
  • 10h30-12h20: Special Interest Topic #10 - Protein Exceptions to the HPP Guidelines (cont)
  • 12h20 End. Exhibit hall teardown

Additional Potential Pitches:

  • Achieving universal implementation of data standards (Andy Jones)
  • Mapping peptides to proteomes considering variants (Luis Mendoza)
  • Implementing the PSI Extended FASTA Format (PEFF) (Eric Deutsch)
  • JPR Annual Special Issue on Proteomics Informatics Tools (TBC)
  • Gathering evidence for translation of lncRNAs (Eric Deutsch)

Attending Organizers:

  • Eric Deutsch
  • Juan Antonio Vizcaíno
  • Lydie Lane
  • Nuno Bandeira
  • Henning Hermjakob
  • Sandra Orchard
  • Magnus Palmblad
  • EuBIC (

Other Confirmed Participants

  • Olga Vitek
  • David Fenyö
  • Lukas Käll
  • Gil Omenn
  • Luis Mendoza
  • All others are welcome!

Special Planned Topics:


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