MIND Informatics develops and applies integrative computational methods in biomedical and brain research, working with leading clinicians and researchers to understand and cure neurological disorders.

Science Collaboration Framework

The Science Collaboration Framework (SCF) is a software toolkit to establish web-based virtual team organizations for researchers in biomedicine. It enables researchers to publish and discuss on-line content such as articles, news, and perspectives, and to provide shared semantic context for this content using established scientific vocabularies.

SCF is reusable open source software based on the popular Drupal content management system, with many new modules to support biomedical researchers and access to RDF "linked data". SCF supports scientists in publishing, annotating, sharing and discussing content such as articles, perspectives, interviews and news items, as well as providing personal biographies, formal and informal bibliographies, and asserting research interests. It also supports shared databases of key research resources, and private research workspaces.

Drupal - the foundation of SCF - is highly extensible and has a thriving ecosystem of contributed modules. SCF includes new contributed Drupal modules for managing publications, interviews, member information, news items, announcements, and biological entities (e.g., genes). It can also read and write RDF "linked data" for cross-community semantic interoperability. SCF is freely available as a Drupal distribution, and the modules can be used a la carte as well.

SCF is a project of the Massachusetts General Hospital and started in collaboration with the Initiative in Innovative Computing at Harvard University, the Digital Enterprise Research Institute, and the Harvard Stem Cell Institute.

SCF web materials can be linked to external, heterogeneous knowledge repositories of life science resources such as genes, antibodies, cell-lines or model organisms. SCF supports structured Web 2.0 style community discourse amongst researchers, makes various data resources available to the collaborating scientist, and captures the semantics of the relationship among the discourse and resources.

SCF supports the following flagship projects:

  • StemBook– a comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to Stem Cell Biology.
  • Pain Research Forum  – a website to enhance collaboration and communication among medical scientists engaged in pain research and therapy
  • Multiple Sclerosis Discovery Forum - a website for news, research and networking among Multiple Sclerosis researchers.

Publications

  • Sudeshna Das, Tom Green, Louis Weitzman, Alister Lewis-Bowen & Tim Clark. Linked Data in a Scientific Collaboration Framework. 17th International World Wide Web Conference (WWW2008), Beijing, China
  • Das S, Girard L, Green T, Weitzman L, Lewis-Bowen A, Clark T. Building biomedical web communities using a semantically aware content management system. Brief Bioinform. 2009 Mar;10(2):129-38. Epub 2008 Dec 6. PMID 19060302.
  • Das S, McCaffrey PG, Talkington MW, Andrews NA, Corlosquet S, Ivinson AJ, Clark T. Pain Research Forum: application of scientific social media frameworks in neuroscience. Front Neuroinform. 2014 Mar 11;8:21. doi: 10.3389/fninf.2014.00021. eCollection 2014. PMID 24653693