Sean, tumbling

Thomas Girke Bioinformatics Workshop materials

Fri, 29 Apr 2011 15:21:39 -0400

Thomas Girke Bioinformatics Workshop materials

de novo assembly technical note from Illumina

Thu, 28 Apr 2011 11:21:44 -0400

de novo assembly technical note from Illumina:

This little PDF is not a bad overview of assemblers and genome assembly for short-read technologies.

myExperiment workflow social networking

Fri, 08 Apr 2011 11:25:37 -0400

myExperiment workflow social networking:

myExperiment makes it easy to find, use and share scientific workflows and other Research Objects, and to build communities.

Taverna - open source and domain independent Workflow Management System

Fri, 08 Apr 2011 11:24:52 -0400

Taverna - open source and domain independent Workflow Management System:

Taverna is an open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation.

Overview of sequencing statistics

Fri, 01 Apr 2011 22:27:00 -0400

Overview of sequencing statistics:

This link is a great PDF of slides from a talk by Mark DePristo from the Broad.

INF 389 - Selected topics in bioinformatics fall 2010: Bioinformatics for high-throughput sequencing

Fri, 25 Mar 2011 14:18:36 -0400

INF 389 - Selected topics in bioinformatics fall 2010: Bioinformatics for high-throughput sequencing:

Here are some nice lecture notes from a course about bioinformatics of high-throughput sequencing.

Sage: Open Source Mathematics Software

Mon, 07 Mar 2011 09:49:53 -0500

Sage: Open Source Mathematics Software:

This is an interesting alternative to mathematica and matlab, implemented in python (+others). Graphing and math abilities look pretty advanced.

Next Generation Genomics: World Map of High-throughput Sequencers

Mon, 07 Mar 2011 07:32:46 -0500

Next Generation Genomics: World Map of High-throughput Sequencers:

This is an interesting page showing world installations of next-gen sequencers on google maps.

Protovis

Sat, 26 Feb 2011 19:53:33 -0500

Protovis:

This is a pretty nice-looking javascript-based data visualization library.

HashBackup: Linux, Mac, FreeBSD/PCBSD Backup

Tue, 22 Feb 2011 21:48:48 -0500

HashBackup: Linux, Mac, FreeBSD/PCBSD Backup:

This tool looks pretty nice for doing backups without much fuss.

Index of /pub/CGP/cosmic/cell_line_export/

Mon, 21 Feb 2011 20:04:16 -0500

Index of /pub/CGP/cosmic/cell_line_export/:

The ftp site for the COSMIC database is tough to find.

"Muchas gracias to Bart’s Blog for this handy reference for svn branches in git. Apparently all..."

Sun, 13 Feb 2011 19:05:53 -0500

“Muchas gracias to Bart’s Blog for this handy reference for svn branches in git. Apparently all I needed was to specify a remote branch when creating the git branch, e.g., git checkout -b git-topic-branch-foo foo
where foo is the name of the remote branch.”

- How do I make git-svn use a particular svn branch as the remote repository? - Stack Overflow

git for projects with large files

Thu, 10 Feb 2011 18:17:37 -0500

git for projects with large files:

I have many projects for which I would like to track “code” but not data, particularly since the data are typically huge. To do this with git, I had been using the model of trying to segregate the…

"Welcome to the Handbook of Biological Statistics! This online textbook evolved from a set of notes..."

Thu, 10 Feb 2011 09:14:17 -0500

“Welcome to the Handbook of Biological Statistics! This online textbook evolved from a set of notes for my Biological Data Analysis class at the University of Delaware. My main goal in that class is to teach biology students how to choose the appropriate statistical test for a particular experiment, then apply that test and interpret the results. I spend relatively little time on the mathematical basis of the tests; for most biologists, statistics is just a useful tool, like a microscope, and knowing the detailed mathematical basis of a statistical test is as unimportant to most biologists as knowing which kinds of glass were used to make a microscope lens. Biologists in very statistics-intensive fields, such as ecology, epidemiology, and systematics, may find this handbook to be a bit superficial for their needs, just as a microscopist using the latest techniques in 4-D, 3-photon confocal microscopy needs to know more about their microscope than someone who’s just counting the hairs on a fly’s back.”

- Handbook of Biological Statistics: Introduction

"Social Media Icons"

Tue, 08 Feb 2011 22:23:48 -0500

“Social Media Icons”

- Social Media Icons — Paul Robert Lloyd

"Sharing your codes in Biocoders.net is very easy, you have to choose the appropriate submitter..."

Sat, 05 Feb 2011 11:42:17 -0500

“Sharing your codes in Biocoders.net is very easy, you have to choose the appropriate submitter either your are coding in R, perl, java or any programming langage you are familiar with. You will be guided through three easy steps before submitting your source codes, we have designed the submitter tool so that we could have as much information as possible on your codes. We welcome any suggestion to make these tools more useful and intuitive.”

- How to use BioCoders submitter tool : BioCoders.net

"Complete Genomics has recently made several complete human genome data sets available. The genomes..."

Thu, 03 Feb 2011 21:58:26 -0500

“Complete Genomics has recently made several complete human genome data sets available. The genomes were sequenced at the Complete Genomics commercial genome sequencing center in Mountain View, California as part of our Complete Genomics Analysis Service (CGA™ Service). These data are largely consistent with the quality and attributes of other data provided to Complete Genomics customers.”

- Complete Genomics » Downloads

Computational Statistics for Genome Biology

Thu, 03 Feb 2011 10:24:20 -0500

Computational Statistics for Genome Biology:

CSAMA 2011: Computational Statistics for Genome Biology (Ninth Edition) This one week intensive course is intended to give insights into recent advances in statistical and computational aspects of the design and interpretation of microarray experiments. The topics will include all aspects of the data analysis of microarray experiments for transcript profiling and ChIP-chip. The course is intended mainly for researchers with a basic understanding of microarray technology and its statistical and computational challenges. The four practical sessions of the course will be most beneficial for participants that are able to converse in a programming language such as R.

What will it cover?

* Introduction to R and Bioconductor
* RNA-Seq and ChiP-Seq data analysis
* Microarray analysis
* Statistics for differential expression
* Sequence manipulation
* Annotation of genes, genomic features and variants
* Gene set enrichment analysis
* Machine Learning
* High-throughput image analysis

ScienceDirect - Cell : An Integrated Approach to Uncover Drivers of Cancer

Wed, 02 Feb 2011 06:05:55 -0500

ScienceDirect - Cell : An Integrated Approach to Uncover Drivers of Cancer:

Yet another “module” paper, but this one is based on copy number and gene expression integration. The method is applied to 62 melanoma samples.

Genome instability: Chrombling into pieces : Article : Nature Reviews Cancer

Tue, 01 Feb 2011 23:07:55 -0500

Genome instability: Chrombling into pieces : Article : Nature Reviews Cancer:

How do multiple chromosomal rearrangements happen simultaneously? See this review and the associated cell paper.