Sorger Lab @ Harvard Medical School

indra

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.

famplex

Resources for grounding protein families and complexes from text and describing their hierarchical relationships.

cycif

Processing and analysys for Cyclic Immunofluorescence (CycIF) microscopy images

palmer-cell-2017

Source code and data for article "Combination cancer therapy can confer benefit via patient-to-patient variability without drug additivity or synergy" by Palmer et al.

OMERO.forms

Extension to OMERO.web to enhance metadata input and provide provenance

bioagents

Biological reasoning agents

pathwaymap.indra.bio

pathwaymap.indra.bio website

CardiotoxDataAnalysis

Data processing and analysis for cardiomyocytes treated with TKIs

cheminformatics_tools

General tools and scripts for cheminformatics analysis and processing

cycif-benchmarking-docker-ashlar

Docker build for benchmarking ASHLAR for AWS Batch

earm

Extrinsic Apoptosis Reaction Model

indra_apps

kegg_metabolite_mapping

lin_elife_2018_tCyCIF_plots

Jupyter Notebook for plotting single-cell data from Lin et al. 2018

omero.cloudarchive-cloudformation

OMERO Cloudarchive Cloudformation

sampattavanich-cellsyst-2018

Source code for the article "Encoding growth factor identity in the temporal dynamics of a transcription factor under combinatorial regulation" by Sampattavanich et al.

2017-10-30-harvard

Website for SWC workshop at Harvard Medical School, October 30-31 2017.

DLSegmenter

Deep Learning based segmentation approach for tCyCIF images

famplex_paper

indra_assembly_paper

Automated assembly of molecular mechanisms at scale from text mining and curated databases

indra_pathway_map

indra_pertbio

lim_pik3ca

analysis for the manuscript_lim et al 2018

omero-ms-image-region-docker

Docker image for image-region OMERO microservice

omero-ms-pixel-buffer-docker

Docker image for pixel-buffer OMERO microservice

omero-nginx-docker

Nginx docker image for OMERO.web

omero-redis-docker

OMERO redis docker image

omero.cloudarchive-docker

OMERO Cloudarchive Docker

QCellCounts

Quality control tool to use during image acquisition for tCyCIF experiments

storage-report-viewer