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.
☆224Jun 30, 2026Updated 3 months ago
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…☆22Jul 9, 2026Updated 3 months ago
- Pathway visualization and analysis tool for Pathway Commons and other BioPAX data☆14May 25, 2022Updated 4 years ago
- Ontology of algorithms for analyzing biological models, their parameters, and their outputs☆12Mar 31, 2026Updated 6 months ago
- Harmonizing pathway databases using Biological Expression Language (BEL)☆20Jul 1, 2024Updated 2 years ago
- 🛣️ Semantic Mapping Reasoning Assembler (SeMRA): tooling for semantic mappings☆17Sep 25, 2026Updated 2 weeks ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- PyBioPAX: A python implementation of the BioPAX object model☆27May 10, 2024Updated 2 years ago
- 🗺️ Community curated and predicted equivalences and related mappings between named biological entities that are not available from prima…☆66Sep 18, 2026Updated 3 weeks ago
- Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML☆28Mar 13, 2023Updated 3 years ago
- A project to capture biological pathway data from academic papers☆29Mar 24, 2025Updated last year
- MOCCASIN translates basic ODE-based MATLAB models of biological processes into SBML format.☆13Aug 21, 2024Updated 2 years ago
- A Python Framework for Modeling and Analysis of Signaling Systems☆30Updated this week
- Grounding of biomedical named entities with contextual disambiguation☆56Jun 29, 2026Updated 3 months ago
- 🐸 Idiomatic conversion between URIs and compact URIs (CURIEs) in Python☆28Sep 29, 2026Updated last week
- 📮 An integrative registry of biological databases, ontologies, and nomenclatures.☆152Updated this week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Python package for working with PEtab files☆18Sep 22, 2026Updated 2 weeks ago
- 📖 Generation and Applications of Knowledge Graphs in Systems and Networks Biology☆33Dec 16, 2019Updated 6 years ago
- Schema for chemistry ontology classes☆24Updated this week
- Python framework for Systems Biology modeling☆201May 19, 2026Updated 4 months ago
- Repository for Apollo-SV ontology. Versioning Apollo-SV independently of the software was made easiest by having it as a separate reposi…☆11Aug 15, 2026Updated last month
- 📛 A Python package for using ontologies, terminologies, and biomedical nomenclatures☆77Sep 23, 2026Updated 2 weeks ago
- 🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)☆139Jul 2, 2026Updated 3 months ago
- ☆71Sep 3, 2026Updated last month
- cy3sbml: SBML for Cytoscape 3☆16Updated this week
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- RO is an ontology of relations for use with biological ontologies☆113Updated this week
- A collection of mathematical models with experimental data in the PEtab format as benchmark problems in order to evaluate new and existin…☆35Sep 29, 2026Updated last week
- 👁️🗨️ Scientists often do the same bad stuff. Automate giving deterministic feedback during peer review with determinstic (LLM-free)☆32May 9, 2025Updated last year
- Software for analyzing high dimensional dose-response data☆19Mar 18, 2026Updated 6 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…☆14May 16, 2023Updated 3 years ago
- Python utilities for SBML☆42Updated this week
- Python parser for UCUM (Unified Code for Units of Measure) incl. converter to pint units☆17Aug 1, 2026Updated 2 months ago
- Schema and generated objects for biolink data model and upper ontology☆265Updated this week
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- 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…☆28Dec 3, 2025Updated 10 months ago
- PSI-MOD ontology for modified and unmodified amino acid residues☆16Sep 18, 2026Updated 3 weeks ago
- python Parameter EStimation TOolbox