Reconstruction algorithms for Python
☆26Oct 23, 2024Updated last year
Alternatives and similar repositories for troppo
Users that are interested in troppo are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- The generic genome-scale metabolic model of Homo sapiens☆171Aug 19, 2026Updated last week
- Constraint-based modeling framework for the enumeration of pathway analysis concepts☆14Jul 6, 2023Updated 3 years ago
- Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method. Also chec…☆17Feb 28, 2025Updated last year
- An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al☆26Jul 15, 2024Updated 2 years ago
- A Python Library to interact with the Cell Collective API v2☆12Dec 8, 2022Updated 3 years 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.
- framed: a metabolic modeling package for python☆26Nov 7, 2019Updated 6 years ago
- An integrated visual environment for metabolic modeling methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as…☆70Aug 15, 2026Updated 2 weeks ago
- D3.js based visualizations of cobrapy metabolic models☆52Mar 10, 2020Updated 6 years ago
- The consensus GEM for Saccharomyces cerevisiae☆133Updated this week
- Secretory Pathway Reconstruction for Human, CHO, and Mouse☆12Aug 24, 2021Updated 5 years ago
- ☆10Jul 21, 2022Updated 4 years ago
- NP classifier using torch and lightning☆23Jun 1, 2026Updated 3 months ago
- ☆11Apr 26, 2021Updated 5 years ago
- ☆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.
- Python package for creating, calibrating and simulating RBA models☆14Aug 19, 2026Updated last week
- An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks.☆16Oct 19, 2022Updated 3 years ago
- PyBoolNet is a Python package for the generation, modification and analysis of Boolean networks.☆55Mar 3, 2026Updated 5 months ago
- SMETANA: a tool to analyse interactions in microbial communities☆74May 6, 2025Updated last year
- ☆19Feb 24, 2016Updated 10 years ago
- novoStoic2.0: Integrated Pathway Design Tool with Thermodynamic Considerations and Enzyme Selection☆11Apr 28, 2025Updated last year
- Using MASST or fastMASST, adding metadata onto a tree ontology for microbes☆27Aug 14, 2026Updated 2 weeks ago
- A python library for accessing 2bit files☆21Apr 21, 2026Updated 4 months ago
- Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.☆25Jul 28, 2026Updated last month
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- A simple tool to predict the general toxicity and calculate the synthesize accessibility (SA) score for small molecules.☆51May 7, 2025Updated last year
- Implements the blood brain barrier score described in: J. Med. Chem. 2019, 62, 21, 9824-9836 (https://doi.org/10.1021/acs.jmedchem.9b0122…☆14Sep 27, 2020Updated 5 years ago
- Mapping-Assisted Targeted-Assembly for Metagenomics☆27Mar 28, 2025Updated last year
- CobraMod is a Python 3 open-source package which enables modifying and extending genome-scale metabolic models with metabolic pathway inf…☆18May 11, 2026Updated 3 months ago
- Workshop in omics integration and systems biology☆89Nov 25, 2024Updated last year
- K-RET: Knowledgeable Biomedical Relation Extraction System☆11Feb 22, 2025Updated last year
- Efficient random sampling for COBRA models☆14Oct 14, 2021Updated 4 years ago
- The standard for open-source GEMs on GitHub☆22Aug 17, 2026Updated 2 weeks ago
- Restructuring of Essential Oil Database☆13Sep 10, 2019Updated 6 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- ☆13Jan 30, 2025Updated last year
- PaNeV: an R package for a pathway-based network visualization☆10Aug 25, 2025Updated last year
- A Python package for "classic" Constraint-Based Reconstruction and Analysis (COBRA) and the new COBRA with kinetics (COBRA-k). Link to do…☆20Jul 16, 2026Updated last month
- R package to Import and Modify SVG (XML) Graphic Files☆28Nov 1, 2024Updated last year
- The binning tool with dynamic contrastive learning and deep language model☆25Aug 14, 2026Updated 2 weeks ago
- Retrieve and normalize records from ICTRP☆10May 26, 2020Updated 6 years ago
- Linking MAGs with 16S rRNA marker genes☆27Feb 8, 2025Updated last year