openjdk:8 based release of CANU, a PacBio assembler

various tools that help with deep sequencing analysis

Designer three layered wireframe DNA origami

Computer Science B.Sc thesis paper and final stage experience. Approaching a Computational Biology Problem with integer linear programming tools.

BLAST wrapper for python that handles circular sequences

This was a project for my bioinformatics class. We studied the circular string problem and its application to bioinformatics and sequence generation / reconstruction. This project solves the circular string problem taking in an integer k, by creating a DeBruijn graph and generating a Euler cycle from it (the edges corresponding to all possible b…

Implementation of random algorithms

DNAc is a programming language for DNAs.

Scripts and pipelines by Merce Montoliu-Nerin

🔮 Predict DNA assembly clone validity rates - powered by Kappa

Open source web app for DNA design and management

The repository contains the source code of the NanoForms server (Czmil et al. NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology. PeerJ, 2022). It is meant to be the source for standalone server installation. https://doi.org/10.7717/peerj.13056

Download the full iGEM database of parts

Online de novo DNA assembly

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

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

🔗 Short overhangs design for DNA assembly

💣 Identify elements impairing success accross group experiments.

Creates a construct developed by the Niles Lab at MIT, designed to deliver a 3' UTR post-transcriptional regulatory element payload to a specific given gene in Plasmodium falciparum.

✂️ Design compact restriction sites arrays (python utility)