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Minerva Python Library
INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
General tools and scripts for cheminformatics analysis and processing
Resources for grounding biological entities from text and describing their hierarchical relationships.
cycif.org GitHub Pages Website
Minerva database components
ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
Jupyter Notebook for plotting single-cell data from Lin et al. 2018
Biological reasoning agents
Deployment of lmod modules and underpinning software on O2
Minimal Docker image based on Alpine Linux
Bio-Formats Directory Scanner
Processing and analysys for Cyclic Immunofluorescence (CycIF) microscopy images
Data processing and analysis for cardiomyocytes treated with TKIs
Repository for OMERO related scripts
BioFormats Tools Docker Image
Docker build for benchmarking ASHLAR for AWS Batch
Source code for the article "Encoding growth factor identity in the temporal dynamics of a transcription factor under combinatorial regulation" by Sampattavanich et al.