Jeremy Muhlich serves as the Director of Software Engineering in the Laboratory of Systems Pharmacology (LSP) at Harvard Medical School. He is a Research Associate in the Harvard Program in Therapeutic Science (HiTS). He oversees software development in the lab at large, with a particular focus on three topics: Building models of cellular signaling networks, microscopy image analysis and visualization, and management and sharing of complex experimental data.
His research into cell signaling modeling led to the creation of PySB, a framework for creating biological models as programs in the Python programming language using a high‐level, action‐oriented vocabulary that promotes transparency, extensibility and reusability. PySB is open-source and its development is hosted at GitHub.
The LSP has a strong focus on high-throughput microscopy, a technique which generates large amounts of data on cellular signaling, protein expression and morphology at a single-cell level. However unlocking this data requires extensive computational processing as well as thoughtful visualization of the results to tie them back to the actual images. Jeremy is currently working on components of the informatics pipeline for the tissue-CyCIF multiplexed immunofluorescence imaging protocol: Ashlar, a tool for merging the many "tiles" and "layers" of images required for the method into seamless mosaic images, and the cycif.org data viewer, a high-performance web-based browser for gigapixel-scale many-channel images.
His data management work aims to simplify the collection, analysis and sharing of large-scale multi-factorial perturbational biological experiments, such as those proposed by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. This research ranges from defining general data standards and best practices, to building software tools implementing those standards, through the creation of custom interactive environments for publishing individual data sets on the web (for examples of the latter, see the HMS LINCS website).