Software
- CellRepo: Cloud-based version control system for digital twins in bioengineering, cellrepo.ico2s.org (L. Hobbs);
- Bakodo: A Ruby gem that is capable of calculating DNA barcodes and their digital equivalents for use in CellRepo (L. Hobbs);
- Contactmap: Convert oxDNA and scadnano formats to origami contact maps, manipulate contact maps, and render faux-geometry of contact maps in 2D/3D via web browser, https://bitbucket.org/engineering-data-structure-organoids/contactmap (Ben Shirt-Ediss);
- Revnano: Reverse engineer origami contact map and domain-level graph from just scaffold and staple sequences, https://bitbucket.org/engineering-data-structure-organoids/revnano (Ben Shirt-Ediss);
- dlprecalc: Perform all pre-calculations for an origami before self-assembly simulation using dlfold, https://bitbucket.org/engineering-data-structure-organoids/dlprecalc (Ben Shirt-Ediss);
- Dlfold: Domain-level kinetic folding simulation of DNA and RNA origami, https://bitbucket.org/engineering-data-structure-organoids/dlfold (Ben Shirt-Ediss);
- dlrender2d: Render origami contact maps as 2D spring layouts and make origami folding MPEG movies, https://bitbucket.org/engineering-data-structure-organoids/dlrender2d (Ben Shirt-Ediss);
- Seqselector: Multi-objective sequence selector for DNA origami nanostructures, https://bitbucket.org/engineering-data-structure-organoids/seqselector (Ben Shirt-Ediss);
- 14origami: Set of 14 diverse origamis used with the multi-objective sequence Selector, https://bitbucket.org/engineering-data-structure-organoids/14origami (Ben Shirt-Ediss);
- Dnaqueue: Stochastic chemical kinetics model of DNA queue polymer chemistry, https://bitbucket.org/engineering-data-structure-organoids/dnaqueue (Ben Shirt-Ediss);
- Dnastack: Stochastic chemical kinetics model of DNA stack polymer chemistry (stacks have X and Y signals), https://bitbucket.org/engineering-data-structure-organoids/dnastack (Ben Shirt-Ediss);
- dnastack-uvkinetics: Docs and scripts for determining DNA stack hybridisation rates from UV absorbance data fitting, https://bitbucket.org/engineering-data-structure-organoids/dnastack-uvkinetics(Ben Shirt-Ediss);
- dna-nanotech-param-fitting: New method to fit DNA chemical reaction rate constants from multiple noisy polyacrylamide gel images, https://bitbucket.org/engineering-data-structure-organoids/dna-nanotech-param-fitting (Ben Shirt-Ediss);
- Circadian: A model for the Kai protein post-translational oscillator in E.coli, https://code.ico2s.org/circadian(Ben Shirt-Ediss);
- ROTC system: algorithm to identify biomarker genes associated with specific stress conditions in bacteria. https://github.com/intbio-ncl/ROTc (David Markham, Anil Wipat);
- mcSTACK: a CTMC-based model checker for DNA stack system (Bowen Li), https://github.com/shelllbw/mcSTACK;
- https://bitbucket.org/JordanConnolly/dna-origami-dataset/src/master/ (Jordon Conolly)
- Source Code bioinformatics paper https://github.com/chang88ye/NIHBA (Shouyong Jiang);
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OptDesign: Computational tool for metabolic network design to improve production; https://github.com/chang88ye/OptDesign (Shouyong Jiang);
- Codes used in paper ‘Computational strategies for the identification of transcriptional biomarker panels to sense cellular growth states in Bacillus subtilis‘; https://github.com/neverbehym/transcriptional-biomarkers-subtilis; created byWe designed a set of computational strategies to identify a few key genes indicative of cellular growth state in bacteria via data mining on bacteria condition-dependent transcriptomes. It can (i) construct a transcriptional landscape capturing the transcriptome shifts under conditions where similar transcriptional states were positioned close; (ii) discover clusters of samples to represent distinct transcriptional states which correlates with cellular growth state in the landscape; (iii) identify reduced sets of biomarker genes that can pinpoint the cluster in the landscape.(Yiming Huang);