Bioinformatics Hub

Bioinformatics Hub

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 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 #HUPO2019

Bioinformatics Hub Schedule:

Monday September 16:

  • 08h30-10h00: Session #1 – Draft MassIVE input into HPP (Nuno Bandeira, UCSD)
  • 10h30-11h00: Session #2a – How to contribute to the C-HPP wiki (Peter Horvatovich, Univ. of Groningen)
  • 11h00-12h30: Session #2b – Stranded and Singleton Peptides (Tadashi Yamamoto, Niigata University; Gil Omenn, U Michigan)
  • 12h30-14h00: Lunch break
  • 14h00-15h15: Session #3 – Human Membrane Proteome Tryptic Peptide Predictor (Subash Adhikari, Macquarie University)
  • 15h15-16h00: Session #4a – The need for bioinformatics tools in clinical settings (Ferdinando Cerciello, University Hospital of Bern, Inselspital)
  • 16h00-17h15: Session #4b – Current advances in DIA data analysis (Brian Searle, ISB)
  • 17h15-19h15: Session #5 – HPP Data Interpretation Guidelines 3.0 (Eric Deutsch, ISB) bioRxiv

Tuesday September 17:

  • 08h30-10h00: Session #6 – Quantifying the impact of public omics data” (Henning Hermjakob, EBI, Juan Antonio Vizcaíno, EBI)
  • 10h30-12h30: Session #7 – (probably no event due to concurrent bioinformatics session)
  • 12h30-14h00: Lunch break
  • 14h00-15h15: Session #8 – SPARQL hands-on session (Lydie Lane, SIB)
  • 15h15-16h00: Session #9a – Open
  • 16h00-17h15: Session #9b – Computational predictions for uPE1 protein functional annotation with I-TASSER and COFACTOR (Gil Omenn, U Michigan; Lydie Lane, SIB; Chengxin Zhang, U Michigan; Yang Zhang, U Michigan )
  • 17h15-18h30: Ask the Experts session

Wednesday September 18:

  • 08h30-10h00: Session #10 – MS Pillar 96-phosphopeptides standard assay results (Sue Weintraub, UTHSCSA; Michael Hoopmann, ISB)
  • 10h00-11h00: Session #11 – EuBIC (European Bioinformatics Community) Intro, discussion, developers meeting(Julian Uszkoreit, Uni. Bochum; Tim Van Den Bossche, Ghent Univ.)
  • 11h00-12h00: Session #12 – Emerging PSI Standards: PEFF, USI, PROXI, SpecLib format (Eric Deutsch, ISB, Juan Antonio Vizcaíno, EBI, Nuno Bandeira, UCSD, Luis Mendoza, ISB)
  • 12h00 End. Exhibit hall teardown

Special Interest Topics to be scheduled:

  • HPP Data Interpretation Guidelines 3.0 (Eric Deutsch, ISB) bioRxiv
  • EuBIC session (Julian Uszkoreit, Uni. Bochum; Tim Van Den Bossche, Ghent Univ.)
  • Human Membrane Proteome Tryptic Peptide Predicter (Subash Adhikari, Macquarie University)
  • MS Pillar 96-phosphopeptides standard assay results (Sue Weintraub, UTHSCSA)
  • Computational predictions for uPE1 protein functional annotation with I-TASSER and COFACTOR (Gil Omenn, U Michigan)
  • Stranded and Singleton Peptides (Tadashi Yamamoto, Niigata University; Gil Omenn, U Michigan)
  • SPARQL hands-on session (Lydie Lane, SIB)
  • Draft MassIVE input into HPP (Nuno Bandeira, UCSD)
  • PSI Standards in progress: PEFF, USI, SpecLib, PROXI (Eric Deutsch, ISB; Juan Antonio Vizcaíno, EBI; Nuno Bandeira, UCSD, Luis Mendoza, ISB)

Attending Organizers:

  • Eric Deutsch
  • Juan Antonio Vizcaíno
  • Lydie Lane
  • Nuno Bandeira
  • Henning Hermjakob
  • Sandra Orchard
  • EuBIC (proteomics-academy.org)
  • Julian Uszkoreit
  • Tim Van Den Bossche

Ask the Experts

  • Brian Searle
  • Sandra Orchard
  • Luis Mendoza

Other Confirmed Participants

  • Gil Omenn
  • Luis Mendoza
  • Subash Adhikari
  • All others are welcome!