November 2, 2016

Links

tamagres-150x70Texas A&M Links


AgriLife/TEES Center for Bioinformatics and Genomic Systems Engineering (CBGSE)
The TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering (CBGSE) functions in the general areas of bionformatics, computational and systems biology. As a cooperative effort between AgriLife and TEES, it constitute both an active research group and a cross-institution graduate student training program focused on plant genomics. CBGSE job site

Texas A&M AgriLife Research
Texas A&M AgriLife Research is the state’s premier research agency in agriculture, natural resources, and the life sciences. They conduct hundreds of projects spanning many scientific disciplines to deliver life-sustaining and industry-changing impact

Texas A&M Supercomputing Facility
The computer systems managed by the Supercomputing Facility are available for use to university faculty, staff, and students who require large-scale computing capabilities.

Texas A&M University System
The Texas A&M University System is one of the largest systems of higher education in the nation, with a statewide network of 11 universities, seven state agencies, two service units and a comprehensive health science center.


Outside Links

ArXiv.org
Preprint publication site for Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics

BioPython
Biopython is a set of freely available tools for biological computation written in Python

BioRxiv.org
BioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory

BioStar
This site’s focus is bioinformatics, computational genomics and biological data analysis questions. We welcome posts that are: detailed and specific, written clearly and simply. No question is too trivial or too “newbie”.

Bits of DNA- Lior Pachter Blog
Berkeley professor Lior Pachter’s blog- The purpose of this site is to supplement my academic website with updates on my research and teaching activities, along with reviews and commentary on current topics in computational biology.

Blue Collar Bioinformatics
Working in the bioinformatics core at Harvard School of Public Health. My main focus is on supporting researchers and creatively answering interesting biological questions. This blog will appeal to those dealing with the practical problems

Casey Bergman- Computational Biology Blog
Top N Reasons To Do A Ph.D. or Post-Doc in Bioinformatics/Computational Biology

Enseqlopedia
Meant to be an encylopedia for NGS. Over time it will be added to so it holds a comprehensive summary of NGS information including: technology providers, methods and applications, people and papers. The blog content will focus on commentary around recent NGS news, new product information and will have an emphasis on technology, advances in NGS and NGS R&D.

Ewan Birney Blog
Blog of Ewan Birney of Director of EMBL-EBI

Galaxy Training Network
There are many resources available that are helpful for teaching Galaxy. This page attempts to summarize them in one location. This page links to workshop materials for different topics. That material can be in this wiki, inside Galaxy instances, or anyw

GATK
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong e

GitHub
GitHub is a web-based hosting service for software development projects that use the Git revision control system. GitHub offers both paid plans for private repositories, and free accounts for open source projects.

Heng Li Blog
My name is Heng Li, a research scientist at the Broad Institute. My current interests include the analysis of new sequencing data, population genetics and phylogenetics.

ISCB
Online Courses in Bioinformatics

Istvan Albert’s Bioinformatics Course
Istvan Albert at Penn State: Applied Bioinformatics Class Notes 2015. Graduate Certificate in Applied Bioinformatics offered via the PSU World Campus. Currently he serves as director for this program.

John Hopkins -Genomic Data Sciences Courses
This specialization covers the concepts and tools to understand, analyze, and interpret data from next generation sequencing experiments. It teaches the most common tools used in genomic data science including how to use the command line, Python, R, Bioco

Living in an Ivory Basement
Stochastic thoughts on science, testing, and programming.

MIT OpenCourseWare
MIT OpenCourseWare (OCW) is a web-based publication of virtually all MIT course content. OCW is open and available to the world and is a permanent MIT activity.

My Biosoftware Blog
My Biosoftware Blog supplies free bioinformatics software for biology scientist, every day.

Nanopore Publications
A list of publications related to Nanopore Sequencing

NextGenSeek
Next Gen Seek: A New Kid in the Block Next generation sequencing technologies have begun to totally revamp the way high-throughput biology is done and it is slowly knocking the doors of hospitals.

Notes on Population Genetics
Graham Coop-Class notes for population genetics

Online Illumina Course
Illumina provides a number of short courses covering Illumina sequencing technology, bioinformatics, and laboratory processes.

Opiniomics
Home of Mick Watson – Bioinformatics, genomes, biology etc. “I don’t mean to sound angry and cynical, but I am, so that’s how it comes across”

Omics! Omics! A computational biologist’s personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery

Philip Guo Blog
Great advice on being a new faculty in data science and advice for students wanting to work in this area. Look around alot of excellent information

R Project
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.

RNASeq Bioinformatics Tools
RNA-Seq is a technique that allows transcriptome studies based on next-generation sequencing technologies. This technique is largely dependent on bioinformatics tools developed to support the different steps of the process. Here are a list

SEQAnswers
One of the oldest NGS forms on the web – always a good place to start

Software Carpentry
Scientific computing doesn’t have to hurt.

Stephen Turner Blog
Great Bioinformatics information site by Stephen Turner, List of Online bioinformatics training resources, presentations, and blogs about bioinformatics

Trapnell Lab
We also study the role of cell-cell communication in governing these processes. We aim to identify genes that control cellular transitions, primarily using single-cell genomics.

TxGen Github site
We provide next generation sequencing and bioinformatics services to scientists across the Texas A&M System and the World.

TxGen Figshare
Complete list of 3000 bioinformatics and computational biology job descriptions

TxGen Youtube
Watch the course lectures of Dr. Datta, Director CBGSE. TxGen was featured on the TAMU ECE promotional video.

Texas A&M grad student RNASeq class

Twitter @BioMath
Genomics and Bioinformatics tweets

Twitter @TxGenJobs
The twitter feed for the TxGene jobs page.

Twitter Feed Amplicon-seq
A PubMed RSS feed for amplicon-seq

Twitter Feed ChIP_seq
A PubMed RSS feed for ChIP-seq studies

Twitter Feed Exome Seq
A PubMed RSS feed for exome related publications

Twitter Feed NIH Funding
Updates from the National Institutes of Health Office of Extramural Research

Twitter Feed RNA_seq
A PubMed RSS feed for RNA-seq related studies

Twitter @TxGen
The twitter feed for the AgriLife Genomics and Bioinformatics Service

About.me @charliejohnson
Dr. Charles Johnson’s About.me site