Microsoft Biology Foundation Use Cases

The Microsoft Biology Foundation (MBF) is an open source, community-curated library of basic bioinformatics functions to simplify the creation of new genomics tools. The use cases below showcase how scientific programmers in industry and academia use MBF to advance their research. You can learn more and download the library and tools for free from the project site.

Johnson & Johnson Pharmaceutical Research & Development

Analysts at J&J PRD have integrated MBF into a data-analysis and visualization platform, Third Dimension Explorer, developed in house at J&J PRD. The Third Dimension Explorer sequence viewer extension enables users to view data in different forms and correlate it directly to the sequence where the data originated. With the help of MBF this tool achieves five distinct tasks:

  • View sequences with their associated assay data to see how variations across compounds impact targets
  • Align multiple sequences
  • View aligned sequences and their associated metadata
  • Extract and translate regions of sequences
  • Work with sequences of different formats to provide a generic platform for scientists to import and analyze them in one place

“[MBF] allowed us to focus on value-added functionality for our scientists and has helped us adapt to new requests quite easily,” says Jeremy Kolpak, J&J PRD senior analyst. Learn more...

Indiana University

“MBF sequence alignment algorithms are used in a parallel (Microsoft HPCS) MPI code to compute the alignment of sets of sequences," says Dr. Judy Qiu, Assistant Professor, School of Informatics & Computing at Indiana University. "The two algorithms we have used so far are the local sequence alignment of Smith-Waterman and global sequence alignment of Needleman-Wunsch. We have extended the set of the built-in similarity scoring matrices in MBF by providing the functionality to load any standard scoring matrix from file. We have also used several utility functions of MBF like FASTA parser to perform initial parsing of sequences from file. The software has worked excellently and we did not find elsewhere the same full suite of capabilities offered by MBF.”

McGill University

BLAST in Pivot, or BL!P, uses the Microsoft Biology Foundation (MBF) open-source bioinformatics toolkit to parse, manipulate, and analyze biological sequence data," says Vince Forgetta, PhD Candidate, Dept. of Human Genetics, McGill University. "Specifically, the FASTA sequence parser is used to parse user-provided biological sequences, and the XML parsers for the BLAST and GenBank formats are used to parse GenBank records and BLAST reports, respectively. MBF is also used to submit the user-provided sequences to the NCBI QBLAST system, query for the status of submitted sequences, and to retrieve completed sequence submissions. MBF has provided an invaluable resource, allowing me to develop bioinformatics software in a reliable and timely manner.”