johnbachman Goto Github PK

adeft

Utility for disambiguating abbreviations in biological texts

asdf_reading_resources

Resources for building machine reading tools in the DARPA ASDF project.

bax_insertion_paper

Code for analyzing and modeling data from an in vitro study of Bax insertion kinetics.

bayessb

bh3_model

Python modeling code for BH3 profiling data

bioagents

Biological reasoning agents

biolit

brain

Resources for assembling and analyzing information about brain research using INDRA.

covid-19

Scripts and other utilities relevant to the CORD-19 dataset

deft_app

simple flask app for grounding lists of terms

depmap_analysis

doctest-ignore-unicode

Nose plugin to ignore unicode literal prefixes in doctests

dorothea

R package to access DoRothEA's regulons

earm

Extrinsic apoptosis reaction model

emcee

The Python ensemble sampling toolkit for affine-invariant MCMC

emmaa

Ecosystem of Machine-maintained Models with Automated Analysis

erk_invitro

estcc

famplex

Namespace encoding hierarchical relationships between proteins, protein families, and protein complexes.

famplex_site

Web site for the FamPlex resource for biology.

flex

A minimalist Pelican theme.

foodome

Code related to the LSP - Barabasi Lab collaboration on understanding molecular mechanisms of food.

genewalk

GeneWalk identifies relevant gene functions for a biological context using network representation learning

hyde

A Python Static Website Generator

idg_ion_channels

Repository for collaboration between the HMS INDRA and IDG Ion Channel teams.

indra

OpenBEL / PySB bridge

indra_apps

indra_curation

A utility build around the HTML assembler to enable easy curation of custom sets of INDRA Statements.

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.

indrabot