Welcome to Christopher Bare

We are excited to announce that Christopher Bare, formerly of the Institute for Systems Biology, has joined Sage Bionetworks as a software engineer supporting the development of Synapse.  Chris has great experience both in the commercial software world, as well as working with visualization, analysis and integration of biological data.  He also happens to write a great technical blog, Digithead’s Lab Notebook, covering programming for the life sciences. Chris joins recent hires Jay Hodgson (Rosetta / Ceiba Solutions) and Eric Wu (Amazon) as we build out the Synapse software engineering team.


Launch of clearScience

We have always envisioned that a key use of the Synapse platform would be to make it easier for researchers to record and document their scientific work in a manner that is easily understandable by others.  This vision just got a boost today with the launch of the clearScience initiative led by Brian Bot and Erich Huang of Sage Bionetworks.  Backed by a generous grant from the Sloan Foundation, the initiative will engage scientific publishers for their ideas on how Synapse can best support scientific communication.  Over the next several months Bot and Huang will be speaking to editors of prominent scientific journals, engaging researchers in a variety of fields, and presenting their evolving ideas at conferences including the upcoming Strata Rx.  And to support the clearScience initiative, Sage’s software team will be accelerating Synapse development for provenance capture and visualization as well as creating scientific narratives that link directly to content managed by Synapse.

If I had a billion dollars…

Guest post from Michael Kellen on incentives and competitions

Science, Reengineered

In an apparently recurring theme, my thoughts again are running to the incentives that drive human behavior, this time inspired by the recent news that the Russian billionaire Yuri Milner has established a new $3 Million Fundamental Physics Prize.  He’s actually awarded 9 of these prizes for a cool $27M promoting the efforts of theoretical physics.  Certainly that kind of money and publicity could drive a lot of attention to the field, and I love the fact that we now almost have a basketball team’s worth of physicists who almost make a basketball player’s salary.

However, is this the best way to spend $27M to shake up and rally support for science?  Of course Mr. Milner is free to spend his money any way he wishes but I see some potential problems with his approach.  Quoting from the NY times article referenced above “Mr. Milner personally selected the inaugural…

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Updated User Profiles Released

We have just released richer public user profiles to capture some basic information about our users (institution, location etc). Your user profile is accessible from the upper-right corner login menu, and is managed separately from your private application settings. You can even populate your Synapse profile by connecting to your Linked-In profile to avoid excess typing.  Our near term goal is to start embedding profile information throughout the site as users do work so we can more visibly highlight and give credit for the contributions people make to open science projects.  Longer term, we hope that collecting and displaying metrics of user contribution to Synapse projects could provide additional ways of demonstrating scientific impact of our users.

Motivating a challenge

Reposted from Michael Kellen’s personal blog

Science, Reengineered

In my previous post I introduced the Breast Cancer Challenge Sage is hosting to build predictive models of the disease.  The initial conception of this project was as a winner take all competition, with a clear scoring method and single top model as the winner of the big prize: publication in Science Translation Medicine.  Compared to some of our other attempts to catalyze scientific collaborations based more on preaching to scientists to share data and methods for the better good of society, this approach seems to have triggered substantially more interest from the community, and action by some of the initial participants.

Our task now is how to best harness this energy to motivate researchers, and also form a community where people not only compete, but also collaborate and build off each other’s work effectively.  Many of my recent discussions with the challenge organizers have drawn analogies to the Tour…

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