- BacilloBricks - Catalogue of parts and their modular, composable models.
- Clotho - Biological engineering tool set for development and management of biological systems
- Converter - Each part from the Registry of Standard Biological Parts (Collection of standardized genetic parts) is available in SBOL format.
- Device Editor - Graphical user interface for J5. J5 is a bioCAD tool that provides rule-based validation of genetic designs that are constructed using SLIC, Gibson, Golden-gate, or CPEC assembly methods.
- Electronic Datasheets - Human- and machine-readable datasheets for the standard biological parts being developed at the BIOFAB
- Eugene - Biological programming language to constrain the composition of genetic parts
- GD-ICE - Laboratory registry software to track and search composable DNA constructs
- GenBank Converter - Interconverts SBOL and Genbank format files.
- Gene Designer - A DNA design tool.
- GenoCAD - Design of synthetic DNA sequences based on grammatical models of genetic part
- iBiosim - Analysis tool for design of genetic circuits and discovery of their connectivity from experimental data
- JBEI-ICE - Repository for DNA sequences, microbial strains, and Arabidopsis seeds.
- j5 - Automates the design of DNA assembly protocols.
- MoSeC - Automates the derivation of DNA sequences from models.
- Proto BioCompiler - Automated design of genetic regulatory networks from high-level programs.
- SBPkb - Knowledgebase of standard biological parts using all the data from the Registry of Standard Biological Parts at MIT.
- TinkerCell - Synthetic biology CAD tool offering drawing and quantitative simulation
- VectorEditor - Viewing, annotating and in silico cloning of sequences