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Synthetic biology

Synthetic biology (SynBio) is a multidisciplinary area of research that seeks to create new biological parts, devices, and systems, or to redesign systems that are already found in nature.

https://github.com/edinburgh-genome-foundry/dnafeaturesviewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

bioinformatics dna-visualization genbank molecular-biology synthetic-biology visualization

Last synced: 21 Dec 2024

https://github.com/ChristophReich1996/Cell-DETR

Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].

attention bibm-2020 cell-detr cell-segmentation deep-learning instance-segmentation synthetic-biology system-biology transformer

Last synced: 13 Nov 2024

https://github.com/edinburgh-genome-foundry/dnacauldron

:alembic: Simple cloning simulator (Golden Gate etc.) for single and combinatorial assemblies

cloning-simulator dna-assembly golden-gate molecular-biology synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/plateo

🤖 Python biolab automation library: parsers, report generators, picklist simulators, and more

lab-automation parser synthetic-biology

Last synced: 18 Dec 2024

https://github.com/edinburgh-genome-foundry/geneblocks

:diamond_shape_with_a_dot_inside: Find common blocks and differences between DNA sequences

python sequence-analysis synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/sequenticon

:space_invader: Generate identicons for DNA sequences with Python

dna-sequences lims sequence-editing synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/primavera

:cherry_blossom: Python library for primer-based verification of DNA assemblies: primer selection, data analyis, etc.

dna-assembly primer-design sequencing synthetic-biology

Last synced: 07 Nov 2024

https://github.com/edinburgh-genome-foundry/crazydoc

Read DNA sequences from colourful Microsoft Word documents

bioinformatics computer-aided-design dna-sequences molecular-biology synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/caravagene

🎨 Python library to plot multi-part genetic constructs

dna-assembly molecular-biology sequence-design synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/genome_collector

:stars: Easily download genomes and build BLAST/Bowtie indexes in Python

bioinformatics blast bowtie ncbi python synbio synthetic-biology taxid

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/bandwagon

🎺 Plot DNA digestion band patterns with Python

agarose-gel dna molecular-biology plotting synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/cuba

🏖️ The EGF Collection of Useful Bio Apps - Web demos of EGF software

django dna-assembly docker-compose sequence-design synthetic-biology vuejs web-development

Last synced: 23 Nov 2024

https://github.com/georgeoshardo/SyMBac

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

biology deep-learning image-processing machine-learning microscopy segmentation synthetic-biology synthetic-data synthetic-dataset-generation

Last synced: 14 Nov 2024

https://github.com/edinburgh-genome-foundry/sbol-visual-css

:curly_loop: Draw genetic elements with HTML & CSS

css sequence-design synthetic-biology user-interface

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/genedom

Batch domestication of genetic parts with Python

dna-assembly part-domestication sequence-design synbio synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/bandwitch

💫 Computer-aided DNA assembly validation and identification from restriction digests.

dna-assembly experimental-design fragment-analysis synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/tatapov

:paw_prints: DNA overhang misannealing data for Python

dna-assembly dna-design golden-gate synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/goldenhinges

:link: Short overhangs design for DNA assembly

dna-assembly sequence-design synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/kappagate

:crystal_ball: Predict DNA assembly clone validity rates - powered by Kappa

biological-simulations dna-assembly kappa-language lab-automation sequence-design synthetic-biology

Last synced: 27 Oct 2024

https://github.com/edinburgh-genome-foundry/zymp

:scissors: Design compact restriction sites arrays (python utility)

dna-assembly restriction-sites sequence-design synthetic-biology

Last synced: 23 Nov 2024

https://github.com/jacobgrisham/synthetic-biology-lims

(In development) Microservices full-stack single-page web app built with Typescript, React, Redux, Styled Components (for CSS-in-JS), Python, Django, Redis, and PostgreSQL. Separate servers for LIMS and Payments hosted on AWS EC2 instances with Kubernetes and circleci CI/CD. Database hosted on AWS DynamoDB. CDN through AWS Cloudfront and DNS through Google Domains.

circleci django django-rest-framework docker docker-compose full-stack-web-development kubernetes lims microservices-architecture postgresql python react redis redux rest-api restful-api styled-components synbio synthetic-biology typescript

Last synced: 21 Oct 2024

https://github.com/JacobGrisham/Synthetic-Biology-LIMS

(In development) Microservices full-stack single-page web app built with Typescript, React, Redux, Styled Components (for CSS-in-JS), Python, Django, Redis, and PostgreSQL. Separate servers for LIMS and Payments hosted on AWS EC2 instances with Kubernetes and circleci CI/CD. Database hosted on AWS DynamoDB. CDN through AWS Cloudfront and DNS through Google Domains.

circleci django django-rest-framework docker docker-compose full-stack-web-development kubernetes lims microservices-architecture postgresql python react redis redux rest-api restful-api styled-components synbio synthetic-biology typescript

Last synced: 08 Nov 2024

https://github.com/edinburgh-genome-foundry/dab

:point_right: EGF Design and Build, the Foundry's DNA design ordering portal

dna-assembly dna-design genome-foundry synthetic-biology

Last synced: 23 Nov 2024

https://github.com/edinburgh-genome-foundry/egf-shared-documents

:books: Shared slideshows, courses, etc. from the EGF

dna-assembly dna-foundry synthetic-biology

Last synced: 23 Nov 2024

https://github.com/ayaanhossain/nrpcalc

Non-Repetitive Parts Calculator - Automated design and discovery of non-repetitive genetic parts for engineering stable genetic systems

algorithm calculator computational-biology cover design discovery finding genetic non-repetitive nrp parts path repeats stable synbio synthetic-biology systems vertex

Last synced: 18 Dec 2024

https://github.com/edinburgh-genome-foundry/icebreaker

:snowflake: Python API for the JBEI-ICE sample manager

jbei-ice lab-automation sample-management synthetic-biology

Last synced: 23 Nov 2024

https://github.com/stracquadaniolab/mooda

A DNA design and assembly method based on multi-objective optimization.

assembly dna-sequence evolutionary-algorithms optimisation synthetic-biology

Last synced: 12 Oct 2024

https://github.com/zulko/bricks_and_scissors

Blog on the computational side of synthetic biology and DNA manufacturing

blog computational-biology genetic-engineering synbio synthetic-biology

Last synced: 14 Nov 2024

https://github.com/gszep/double-exclusive-reporter

Code supplementary for Grant P. et al. 2020. Interpretation of morphogen gradients by a bistable circuit

biophysics julia-language microsoft morphogenesis simulation synthetic-biology

Last synced: 11 Dec 2024

https://github.com/j-e-j-s/aars-pipeline

A Scalable Pipeline for Discovery of aaRS Mutants to Aid in Genetic Code Expansion.

bioengineering bioinformatics biology computational-biology nextflow pipeline python synthetic-biology

Last synced: 16 Dec 2024

https://github.com/moltinginstar/addgene-api

An unofficial API for Addgene, the open-source plasmid repository.

addgene api dna dna-sequences genbank plasmids rna snapgene synthetic-biology unofficial web-scraping

Last synced: 22 Dec 2024

https://github.com/bradyajohnston/reluxr

Deconvolute Luminescence Readings on Bacterial Culture Plates

plate-reader r r-package synthetic-biology

Last synced: 08 Nov 2024

https://github.com/ayaanhossain/oligopool

Oligopool Calculator - Automated design and analysis of oligopool libraries

assembly barcode counter design gibson-assembly golden-gate-cloning motif mpra ngs oligo oligo-design pcr pool primer search spacer synthetic-biology

Last synced: 11 Dec 2024

https://github.com/amorehead/synbio-mat

A repository for mathematical applications in the context of synthetic biology research.

distribution machine-learning optimization pooling probability synthetic-biology

Last synced: 13 Dec 2024

https://github.com/j-e-j-s/gb2fasta

Convert GenBank Files to FASTA Without Leaving the Terminal.

bioinformatics cli synthetic-biology

Last synced: 08 Nov 2024

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