Projects
A collection of personal, academic and professional projects.
J.Seq
A proprietary software part of Just-Evotec's JDesign platform that enables rapid creation of new bioinformatics data pipelines and their execution on serverless cloud nodes. Ties into highly efficient relational database, GraphQL API, a React webapp.
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DASi (BioCAD)
DASi is an automatic DNA cloning plan designer aimed for operating on small budgets by focusing on material re-use and a dead-simple user interface. The software converts a nucleotide sequence, or a library of sequences, to an executable molecular assembly plan while optimizing material cost, assembly efficiency, and assembly time. No molecular biology expertise is required to use DASi. DASi produced plans can be automatically executed using a bio-fabrication facility.
Learn more →Terrarium (BioCAPP)
Terrarium is a dynamic computer-aided process planner (CAPP) for biology designed for agile manufacturing of biological products, such as E Coli & Yeast strains, or Mammalian cell lines. The software automatically plans scientific experiments in Aquarium using historical planning data and current laboratory inventory and solves an MST optimization problem to give optimal and valid operational workflows.
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Aquarium (BioCAM)
The wetlab laboratory "Operating System", Aquarium automatically generate executable lab protocols, lab workflows, stores data, tracks lab processing, and much more. Now open-sourced.
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OLASimple
A simple HIV drug-resistence assay (similar to a stick-based pregnancy test) that includes accompanying software to guide users through the laboratory steps and final analysis image processing to interpret results. Prototyped in Nairobi, Kenya.
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Optogenetics Sensors and Light Delivery System
A programmable light delivery box for optogenetics experiments. This small and cheap light delivery system was used in several publications. Making something that flashes light isn't rocket science, but its important to have a robust, and hardy system for delivering light in a reliable and reproducible way while doing long and expensive optogenetics experiments. Additionally, not having tools for light delivery can be a major roadblock for those new to optogenetics.
Learn more →Small projects
A collection of personal, academic and professional projects.
Pydent
Pydent is the Python scripting API for Aquarium , the software that runs the UW BIOFAB. The code respository is freely available to all.
Learn more →BenchlingAPI
Benchling Python API. An old project the preceded Benchlings official API functionality.
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