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Name: Benedict Paten
Type: User
Company: UCSC
Twitter: benedictpaten
Location: UCSC
Name: Benedict Paten
Type: User
Company: UCSC
Twitter: benedictpaten
Location: UCSC
Library for Assemblathon 1 analysis scripts
Benchmarking scripts for assessing assemblies, used in the Assemblathon 1 project
Class lectures for BME-230B
A home for various common but non-essential scripts for the cactus project
C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.
Little experiments on a better mapq cap function
Lecture Notes and Slides for UCSC CSE20, formatted as Jupyter Notebooks.
Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)
UCSC Nanopore
Library of matching and ordering algorithms, used for "reference problem"
Evolutionary transducer based method for aligning and reconstructing indel histories
Probabilistic consistency based aligner
Library for constructing pinch graphs and cactus graphs
Evaluation scripts for testing cactus progressive method
Prototype implementation of SQG parser in Python
Scripts for evaluating a cactus reference genome
Work on data models and APIs for graph structures that represent the human reference genome plus common human genetic variants. Includes mapping to a reference genome, and standardization of the mechanism for referring to variants.
Work on data models and APIs for Genomic data.
HMM-HDP models for MinION signal alignments
Small general purpose library for C and Python with focus on bioinformatics.
Python based pipeline management software for clusters that makes running recursive and dynamically scheduled computations straightforward. So far works with gridEngine, lsf, parasol and on multi-core machines.
tools for working with variation graphs
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.