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.
☆212May 26, 2026Updated last week
Alternatives and similar repositories for indra
Users that are interested in indra are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- 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…☆19May 22, 2026Updated 2 weeks ago
- Pathway visualization and analysis tool for Pathway Commons and other BioPAX data☆14May 25, 2022Updated 4 years ago
- Resources for grounding protein families and complexes from text and describing their hierarchical relationships.☆18Mar 26, 2026Updated 2 months ago
- Harmonizing pathway databases using Biological Expression Language (BEL)☆20Jul 1, 2024Updated last year
- Ontology of algorithms for analyzing biological models, their parameters, and their outputs☆12Mar 31, 2026Updated 2 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- PyBioPAX: A python implementation of the BioPAX object model☆27May 10, 2024Updated 2 years ago
- A project to capture biological pathway data from academic papers☆29Mar 24, 2025Updated last year
- 🗺️ Community curated and predicted equivalences and related mappings between named biological entities that are not available from prima…☆63May 31, 2026Updated last week
- Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML☆28Mar 13, 2023Updated 3 years ago
- MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.☆13Aug 21, 2024Updated last year
- A Python Framework for Modeling and Analysis of Signaling Systems☆29May 25, 2026Updated 2 weeks ago
- Grounding of biomedical named entities with contextual disambiguation☆53May 29, 2026Updated last week
- PSI-MOD ontology for modified and unmodified amino acid residues☆16May 28, 2026Updated last week
- Ontology for representing scientific evidence and provenance information☆53Oct 2, 2025Updated 8 months ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- 📮 An integrative registry of biological databases, ontologies, and nomenclatures.☆143Updated this week
- 📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology☆33Dec 16, 2019Updated 6 years ago
- Schema for chemistry ontology classes☆23May 22, 2026Updated 2 weeks ago
- Python package for working with PEtab files☆16May 27, 2026Updated last week
- Python framework for Systems Biology modeling☆197May 19, 2026Updated 3 weeks ago
- ☆72May 31, 2022Updated 4 years ago
- 📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures☆76Updated this week
- 🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python☆27May 7, 2026Updated last month
- RO is an ontology of relations for use with biological ontologies☆112Feb 3, 2026Updated 4 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- cy3sbml: SBML for Cytoscape 3☆15Jan 22, 2026Updated 4 months ago
- KGX is a Python library for exchanging Knowledge Graphs☆140Updated this week
- 👁️🗨️ Scientists often do the same bad stuff. Automate giving deterministic feedback during peer review with determinstic (LLM-free)☆30May 9, 2025Updated last year
- Repository for Apollo-SV ontology. Versioning Apollo-SV independently of the software was made easiest by having it as a separate reposi…☆11Apr 9, 2026Updated last month
- Schema and generated objects for biolink data model and upper ontology☆242May 29, 2026Updated last week
- A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existin…☆33Apr 14, 2026Updated last month
- Software for analyzing high dimensional dose-response data☆19Mar 18, 2026Updated 2 months ago
- python library for working with ontologies and ontology associations☆133Feb 11, 2025Updated last year
- The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in part…☆12May 16, 2023Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Tool for disambiguating acronyms and abbreviations in text for NLP applications☆22Mar 26, 2026Updated 2 months ago
- Python utilities for SBML☆41Apr 23, 2026Updated last month
- R package for functionally scoring phosphorylation sites☆23Nov 3, 2019Updated 6 years ago
- The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML suppor…☆27Dec 3, 2025Updated 6 months ago
- Python parser for UCUM (Unified Code for Units of Measure) incl. converter to pint units☆14May 1, 2026Updated last month
- StochKit is an extensible tool for stochastic simulation tool with stochastic and multiscale algorithms.☆17Jun 9, 2020Updated 5 years ago
- python Parameter EStimation TOolbox☆273Updated this week