Pinned Repositories
asdf_reading_resources
Resources for building machine reading tools in the DARPA ASDF project.
depmap_analysis
earm
Extrinsic apoptosis reaction model
famplex
Namespace encoding hierarchical relationships between proteins, protein families, and protein complexes.
indra_pertbio
nf_copper
pysb
Python framework for Systems Biology modeling
johnbachman's Repositories
johnbachman/famplex
Namespace encoding hierarchical relationships between proteins, protein families, and protein complexes.
johnbachman/depmap_analysis
johnbachman/pysb
Python framework for Systems Biology modeling
johnbachman/nf_copper
johnbachman/adeft
Utility for disambiguating abbreviations in biological texts
johnbachman/bax_insertion_paper
Code for analyzing and modeling data from an in vitro study of Bax insertion kinetics.
johnbachman/bioagents
Biological reasoning agents
johnbachman/brain
Resources for assembling and analyzing information about brain research using INDRA.
johnbachman/covid-19
Scripts and other utilities relevant to the CORD-19 dataset
johnbachman/dorothea
R package to access DoRothEA's regulons
johnbachman/emcee
The Python ensemble sampling toolkit for affine-invariant MCMC
johnbachman/emmaa
Ecosystem of Machine-maintained Models with Automated Analysis
johnbachman/genewalk
GeneWalk identifies relevant gene functions for a biological context using network representation learning
johnbachman/idg_ion_channels
Repository for collaboration between the HMS INDRA and IDG Ion Channel teams.
johnbachman/indra
OpenBEL / PySB bridge
johnbachman/indra_apps
johnbachman/indra_curation
A utility build around the HTML assembler to enable easy curation of custom sets of INDRA Statements.
johnbachman/indra_db
A Database-based knowledge back-end built on and for INDRA. The INDRA Database is a service that can be set up by any user with their own content and knowledge access. Our implementation of the database is the back-end to many of our projects, providing a vast and detailed knowledge base derived from many resources.
johnbachman/indra_db_paper
Scripts and Jupyter notebooks for the INDRA Database manuscript.
johnbachman/indra_network_search
REST API for querying the network of biochemical mechanisms in the INDRA DB.
johnbachman/indra_phospho
Tools for analyzing phosphoproteomic data using functional information assembled by INDRA.
johnbachman/indra_reading
Tools used for large scale reading, mostly using AWS Batch.
johnbachman/kinases_motility
Query the INDRA DB for information about kinases that regulate cell motility.
johnbachman/nf_model
Resources for an EMMAA model focusing on molecular mechanisms of neurofibromatosis.
johnbachman/OmicsIntegrator
This repository is the working directory for the Garnet-Forest bundle of python scripts for analyzing diverse forms of 'omic' data in a network context.
johnbachman/paths_graph
A graphical representation of ensembles of paths in directed networks.
johnbachman/protmapper
Map amino acid sites of post-translational modifications from models or data to reference positions.
johnbachman/pybel
A Python package for parsing, validating, and converting BEL networks
johnbachman/pykeen
A Python library for learning and evaluating knowledge graph embeddings
johnbachman/reach
Reach Biomedical Information Extraction