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    55 repositories

    • indra

      Public
      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.
      nlpbioinformaticsbiologymodelingsystems-biologycomputational-biologypysbindrasbml
      Python
      •
      BSD 2-Clause "Simplified" License
      •67•179•33•6•Updated Nov 19, 2024Nov 19, 2024

    • famplex

      Public
      Resources for grounding protein families and complexes from text and describing their hierarchical relationships.
      Python
      •
      Creative Commons Zero v1.0 Universal
      •31•18•28•2•Updated Jul 10, 2024Jul 10, 2024

    • bioagents

      Public
      Biological reasoning agents
      Python
      •
      BSD 2-Clause "Simplified" License
      •15•5•7•2•Updated Apr 3, 2024Apr 3, 2024

    • OMERO.forms

      Public
      Extension to OMERO.web to enhance metadata input and provide provenance
      webappomero
      Python
      •
      GNU Affero General Public License v3.0
      •4•7•4•3•Updated Dec 5, 2023Dec 5, 2023

    • indra_assembly_paper

      Public
      Automated assembly of molecular mechanisms at scale from text mining and curated databases
      Jupyter Notebook
      •1•0•0•1•Updated Jan 23, 2023Jan 23, 2023

    • pathwaymap.indra.bio

      Public
      pathwaymap.indra.bio website
      JavaScript
      •
      BSD 2-Clause "Simplified" License
      •1•2•0•7•Updated May 25, 2022May 25, 2022

    • indra_apps

      Public
      Jupyter Notebook
      •8•1•0•0•Updated Apr 26, 2021Apr 26, 2021

    • earm

      Public
      Extrinsic Apoptosis Reaction Model
      Python
      •17•1•3•1•Updated Oct 28, 2020Oct 28, 2020

    • indra_pathway_map

      Public
      JavaScript
      •
      BSD 2-Clause "Simplified" License
      •5•0•0•0•Updated Jun 17, 2020Jun 17, 2020

    • cycif

      Public
      Processing and analysys for Cyclic Immunofluorescence (CycIF) microscopy images
      MATLAB
      •
      MIT License
      •4•9•0•0•Updated May 5, 2019May 5, 2019

    • cheminformatics_tools

      Public
      General tools and scripts for cheminformatics analysis and processing
      Python
      •
      MIT License
      •2•1•0•0•Updated Mar 18, 2019Mar 18, 2019

    • DLSegmenter

      Public
      Deep Learning based segmentation approach for tCyCIF images
      0•0•0•0•Updated Dec 6, 2018Dec 6, 2018

    • QCellCounts

      Public
      Quality control tool to use during image acquisition for tCyCIF experiments
      0•0•0•0•Updated Dec 6, 2018Dec 6, 2018

    • CardiotoxDataAnalysis

      Public
      Data processing and analysis for cardiomyocytes treated with TKIs
      MATLAB
      •1•1•0•0•Updated Nov 30, 2018Nov 30, 2018

    • lin_elife_2018_tCyCIF_plots

      Public
      Jupyter Notebook for plotting single-cell data from Lin et al. 2018
      Jupyter Notebook
      •
      MIT License
      •3•1•0•0•Updated Oct 19, 2018Oct 19, 2018

    • lim_pik3ca

      Public
      analysis for the manuscript_lim et al 2018
      Jupyter Notebook
      •1•0•0•0•Updated Sep 25, 2018Sep 25, 2018

    • indra_pertbio

      Public
      Python
      •
      MIT License
      •2•0•0•0•Updated Sep 4, 2018Sep 4, 2018

    • storage-report-viewer

      Public
      JavaScript
      •1•0•6•0•Updated Jul 11, 2018Jul 11, 2018

    • famplex_paper

      Public
      Python
      •0•0•0•0•Updated May 11, 2018May 11, 2018

    • cycif-benchmarking-docker-ashlar

      Public
      Docker build for benchmarking ASHLAR for AWS Batch
      dockerawsbenchmarkingcycif
      Python
      •
      MIT License
      •0•1•0•0•Updated Apr 17, 2018Apr 17, 2018

    • sampattavanich-cellsyst-2018

      Public
      Source code for the article "Encoding growth factor identity in the temporal dynamics of a transcription factor under combinatorial regulation" by Sampattavanich et al.
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Mar 16, 2018Mar 16, 2018

    • kegg_metabolite_mapping

      Public
      Python
      •0•1•0•0•Updated Feb 2, 2018Feb 2, 2018

    • omero.cloudarchive-cloudformation

      Public
      OMERO Cloudarchive Cloudformation
      awscloudformationomeroopenmicroscopy
      Shell
      •
      GNU Affero General Public License v3.0
      •1•1•1•0•Updated Jan 2, 2018Jan 2, 2018

    • palmer-cell-2017

      Public
      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.
      Mathematica
      •
      MIT License
      •2•8•0•0•Updated Nov 21, 2017Nov 21, 2017

    • 2017-10-30-harvard

      Public
      Website for SWC workshop at Harvard Medical School, October 30-31 2017.
      Python
      •
      Other
      •0•0•0•0•Updated Oct 30, 2017Oct 30, 2017

    • omero.cloudarchive-docker

      Public
      OMERO Cloudarchive Docker
      awsclouds3openmicroscopydockeromero
      Python
      •
      GNU Affero General Public License v3.0
      •2•0•0•0•Updated Oct 18, 2017Oct 18, 2017

    • omero-nginx-docker

      Public
      Nginx docker image for OMERO.web
      dockernginxomeroomero-web
      Shell
      •4•0•0•0•Updated Oct 18, 2017Oct 18, 2017

    • omero-redis-docker

      Public
      OMERO redis docker image
      Shell
      •0•0•0•0•Updated Oct 18, 2017Oct 18, 2017

    • omero-ms-pixel-buffer-docker

      Public
      Docker image for pixel-buffer OMERO microservice
      dockermicroserviceomero
      Shell
      •0•0•0•0•Updated Aug 25, 2017Aug 25, 2017

    • omero-ms-image-region-docker

      Public
      Docker image for image-region OMERO microservice
      Shell
      •0•0•0•0•Updated Aug 22, 2017Aug 22, 2017