An open source web-based visualization and editing toolkit for do-it-yourself biology (DIYbio).
Access to tools. GPL'd.
- Plasmid & Sequence Editor
- For both circular and linear sequences
- Spec:
- Radial visualization of sequences as features (sub-sequences)
- Visualization interactions, hover, highlight, select
- Effective, visible labels
- Full annotation for each feature , displayed conveniently on hover
- Side-by-side display of radial plasmid visualization and plain text sequences.
- Sequence and feature highlighting
- Insert and delete operations
- Visualization zoom
- Toggles for display components for diagram creation
- Sequence checker
- Diff tool to check, verify, and visualize sequences
- Spec:
- Handles AB1 or ABI files.
- Use Smith-Waterman Algorithm
- Needs both analog line graph output and sequence diffing in plain text
- Use vertical diff (rather than long, side-scrolling horizontal)
- Standard Protocol Format
- Complete set of operations and a grammar to specify and simulate DIYbio practices
- Spec:
- Requires a standard set of operations
- Provides simulation
- Share and re-use protocols
- Possibly generate protocols based on desired results
- Folding prediction
- Tool to identify problematic folds in DNA, RNA, etc
- Codon Switcher
- Switches order of codons to optimize modifications to have lower risk of failure.