We are a team of data management experts and bioinformaticians, who founded the Forome Open Genomics community to accelerate Mendelian diseases diagnostic.
See more at the Forome Association Home Page
AnFiSA is an open-source computational platform for the analysis of sequencing data for rare genetic disease
We have created a fully open-source variant curation tool, AnFiSA, with the intention to invite and accept contributions from clinicians, researchers, and professional software developers. The design of AnFiSA addresses the aforementioned issues via the following architectural principles: using a multidimensional database management system (DBMS) for genomic data to address reproducibility, curated decision trees adaptable to changing clinical rules, and a crowdsourcing-friendly interface to address difficult-to-diagnose cases. We discuss how we have chosen our technology stack and describe the design and implementation of the software. Finally, we show in detail how selected workflows can be implemented using the current version of AnFiSA by a medical geneticist.
See our Research AnFiSA article in the Journal of Biomedical Informatics
See also User Documentation and Anfisa Development Documentation
Deploy repository is your starting point to start using AnFiSA. The easiest way to deploy is to use docker-compose.
To set up development environment, use local deploy.
If you would like to participate in our projects, please contact us. We invite and accept contributions from clinicians, researchers, and professional software developers. Contributions can be made into software source code, documentation, Frequently Asked Questions and as proposals for new use cases.
We also value any feedback regarding the existing functionality, please create a GitHub issue here or contact us with your feedback.
Forome software development has been sponsored by a number of organizations, including Harvard University, IBM Cognitive Cloud and IBM Chicago Center for Advanced Studies, Quantori and others.
When we develop Java code we use JProfiler Java profiler
