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.


MIND Informatics projects encompass both classical biomedical informatics and scientific social media with a special emphasis on ontology development and Semantic Web technologies for integrating and sharing neuroscience research.

The Massachusetts Alzheimer Disease Research Center (MADRC) is one of the world's leading centers for research into the causes, treatment and potential cures for Alzheimer Disease (AD), a devastating neurodegenerative disorder affecting more than 25 million people worldwide. A collaboration between researchers at the Massachusetts General Hospital and Brigham and Women's Hospital, MADRC is funded by a National Institute on Aging P-50 award, as well as private philanthropy. MADRC is one of the oldest research centers in the NIA program.

The Stem Cell Commons (stemcellcommons.org) was initiated by the Harvard Stem Cell Institute to develop a community for stem cell bioinformatics. This open source environment for sharing, processing and analyzing stem cell data brings together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons.

Domeo is an extensible web application enabling users to visually and efficiently create and share ontology-based stand-off annotation on HTML or XML document targets. The tool supports manual, fully automated, and semi-automated annotation with complete provenance records, as well as personal or community annotation with access authorization and control.

Open Annotation of web content means the ability to make notes, attach tags, classify, apply formal semantics, and otherwise annotate any content on the web, whether or not you have update control over the server providing it - and to share those annotations in open format with others.  This capability returns the tradition of scholarly "marginalia" to digital scholarship, at a higher level, using all the technical capabilities of the web.

In biomedical research, it allows among other things, semantic tagging of research publications with gene, protein, chemical compound, pathway, disease, anatomical, cell type, organism, and many other types of information "on the fly", with selected publication and selected uptake of the results. It also allows for new kinds of collaboration such as crowdsourced classification and online vitual journal clubs.

The Pain Research Forum is an interactive virtual community and web-based resource for basic, translational and clinical researchers working to discover new treatments for chronic and neuropathic pain. Open communication and rapid exchange of information speed progress toward new treatments, but the pain research community is fragmented across many disciplines and specialties, each with its own conferences and journals. PRF brings the community together by providing a single venue where researchers can keep up to date with the latest news, access resources and community information, and debate emerging themes and ideas relevant to pain research. The site is a joint project of the Harvard NeuroDiscovery Center—responsible for the content of the site—and the MIND Informatics team at MGH—responsible for web development and maintenance. 

Stem Book is an open access collection of invited, original, peer-reviewed chapters covering a range of topics related to stem cell biology written by top researchers in the field at the Harvard Stem Cell Institute and worldwide. Stem Book is aimed at stem cell and non-specialist researchers. In addition to the contributions of the editorial board and the stem cell research community, the project is being done in collaboration with several other enterprises including Harvard’s Initiative in Innovative Computing. The Initiative in Innovative Computing created the Scientific Collaboration Framework (SCF), the extensible software infrastructure used for the project. SCF and the Stem Book project were funded, in part, by a generous grant from an anonymous foundation and also appreciates the input of WormBase's Textpresso team.

The Multiple Sclerosis Discovery Forum (MSDF) is an online resource that aims to accelerate progress toward cures for multiple sclerosis and related disorders by sparking new ideas and catalyzing unforeseen connections. The site focuses attention on what is known and not yet known about the causes of these conditions, their pathological mechanisms, and potential ways to intervene. By communicating this information in a way that builds bridges among different disciplines, we will open new routes toward significant clinical advances.


eXFrame is a reusable framework for building genomics experiments repositories. eXframe provides 1) the ability to upload structured data compliant with accepted standards 2) support for multiple genomics data types including microarrays and next generation sequencing 3) import/export of data in various formats 4) query, analysis and visualization integration tools enabled by consistent processing of the raw data 5) Linked Data and SPARQL endpoint of the experimental information.

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.

Completed Projects

Past project.

Past project.