San Francisco, 19-20 April 2013

"The Truth of Personalized Medicine: Our Commons Future"

Workgroup E – Platform

(3 Sept 2011) Updates on the post-Congress Workgroup/Community of Interest activities are available in the Sage Bionetworks web site.

Leaders: Mike Kellen & Martin Morgan


The platform builders community is characterized by people who are focused on the informatics infrastructure needed to support the broader Sage Commons effort. These people will mainly come from 3 places:

  1. Software vendors who sell into the pharmaceutical / biotech industry. This includes some large enterprise software companies (Microsoft, Amazon, etc.) along with more industry-specific players (NextBio, Ingenuity, etc.)
    Goal: explore ways in which vendors can integrate their business models and offerings with the Sage open community.
  2. Open source software developers for the life sciences market, mostly from academic and non-profit institutions (Bioconductor, Recombinant Data,etc).
    Goal: identify overlapping efforts and reduce redundancy. Build a community of platform contributors.
  3. Representatives of the IT organizations of pharmaceutical and biotech companies
    Goal: explore the use of the Sage platform by the pharmaceutical industry: pooled investments (finanical or development resources) from several large pharmas could create something more powerful than any company could build alone.

Workshop Program

Part 1: Survey of other efforts (1 hr)
In part 1 of the platform workshop we will hear short presentations from a small subset of the group members. The goal is to have a brief survey of some of the key projects across the bioinformatics landscape and understand how they relate to the Sage platform. Due to time constraints, we will have to limit this section to a small selection of conference participants and will also limit speaking time to 5 minutes per speaker.

Part 2: Break-out discussions (2 hr)
Part 2 is an open discussion forum for participants to help guide the development of the Sage platform. Based on the knowledge the attendees gain of the work at Sage and their previous experience, how should the platform vision be refined? What are the most critical priorities for development? What opportunities for collaboration exist? What are the things to watch out for. Discussions will be focus on these topics:

  • Datasets: How can Sage-hosted data best be made available to other groups for reuse?
  • Tools and Networks: How can existing analysis tools be brought into the platform vision for a shared, hosted computational space?
  • People and Projects: How can the platform facilitate sharing resources across distributed research teams?

Part 3: Summary reports (30 min)
In Part 3 we will reconvene as a large group, with each group having a 10 minutes to report back to the large team a summary of the discussion points and key recommendations.


The main goal of the Congress is to engage the community to help guide development of the platform by Sage, and to identify collaborating efforts that that extend or complement the development efforts of Sage. The workshop should provide some key recommendations for the Sage platform team and opportunities to link with existing efforts.

One Response to “Workgroup E – Platform”

  1. Barry Bunin
    April 12th, 2011 @ 12:04 am

    CDD has linked CDD Public data to and from ChemSpider and would do the same with others, upon request, see the press release here:

    And CDD Public data for commercial, humanitarian, and drug repurposing applications here:

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