background preloader


Facebook Twitter

TCGA Pan-Cancer Analysis. Cell. English Communication for Scientists. MRC National Institute for Medical Research, London. Chronic Myeloid Leukemia Spotlight : Spotlight : Leukemia. Public Library of Bioinformatics. SEQanswers Home.

PLoS articles

Biomarkers and Personalized Medicine. Life Sciences & Mathematics & Physical Sciences. OpenHelix Blog. Home. RHIPE: An Interface Between Hadoop and R for Large and Complex Data Analysis. Ron Fredericks writes: Dr.

RHIPE: An Interface Between Hadoop and R for Large and Complex Data Analysis

Saptarshi Guha created an open-source interface between R and Hadoop called the R and Hadoop Integrated Processing Environment or RHIPE for short. LectureMaker was on the scene filming Saptarshi’s RHIPE presentation to the Bay Area’s useR Group, introduced by Michael E. Driscoll and hosted at Facebook’s Palo Alto office on March 9′th 2010. Special thanks to Jyotsna Paintal for helping me film the event. Saptarshi received his Ph.D from Purdue University in 2010, having been advised by Dr. Hadoop is an open source implementation of both the MapReduce programming model, and the underlying file system Google developed to support web scale data.The MapReduce programming model was designed by Google to enable a clean abstraction between large scale data analysis tasks and the underlying systems challenges involved in ensuring reliable large-scale computation.

The RHIPE Video Video Topics and Navigation Table Code Examples from the Video Code (r) References: Computational Biology Center. Web services for bioinformatics, Part 1. Web services for life sciences The IBM alphaWorks article on web services for life sciences is an example set of web services that offers standard bioinformatics applications and demonstrates the technology (See Resources).

Web services for bioinformatics, Part 1

The project is written in Java and mainly acts as a wrapper around existing bioinformatics applications. It allows researchers to search through the web service and obtain output through XML documents and to view intermediate steps throughout the request. Bioinformatics research applications exist in various stages of completeness in many different languages. Furthermore, building a workflow from several different applications requires installing applications locally, copying input and output data by hand, and often modifying source code for adapting changes in output and input data format. Efficiency, throughput, and workflow are major concerns when considering tools for comparative genomics. Document -style services $ perl WSDL2Perl WSDL-file-URL Listing 2: Types #! #! TikZ and PGF resources. A growing collection of links to various TikZ and PGF resources.

TikZ and PGF resources

Various packages that extends or are built on top of TikZ and PGF. Beamer A LaTeX class for creating presentations. Written by the same author as PGF/TikZ. Bodegraph. Mathematics part 2 - Getting to grips with LaTeX. By Andrew Roberts This tutorial builds on the basic foundations presented in the previous tutorial.

Mathematics part 2 - Getting to grips with LaTeX

If you often include a lot of maths in your documents, then you will probably find that you wish to have slightly more control over presentation issues. Some of the topics covered make writing equations more complex - but who said typesetting mathematics was easy?! Adding text to equations I doubt it will be every day that you will need to include some text within an equation. There are two noticeable problems. There are a number of ways that text can be added properly. The text looks better. Formatted text Using the \mbox is fine and gets the basic result. However, as is the case with LaTeX, there is more than one way to skin a cat!

The maths formatting commands can be wrapped around the entire equation, and not just on the textual elements: they only format letters, numbers, and uppercase Greek, and the rest of the maths syntax is ignored. Changing text size of equations. Bioinformatics Organization - Bioinformatics.Org. Bioinformatics Projects List. November 10: Provide an outline of your work, as well as a preliminary list of references; Develop your presentation skills.

Bioinformatics Projects List

The format of the projects is quite flexible. I foresee three types of work: 3) A review of the literature on a specific topic. For all three types of work, I would expect to see a review of the literature, sample data and a prototype implementation. Teams will be made of 1 to 4 members; the optimum being 2 persons per team. The project is worth 20% of your final mark. .NET Bio. Bioinformatics journal list.


Courses. Kevin Ahern's Wildly Popular Metabolic Melodies. BB 350 Oregon State University. Schedule for BB 350 Ecampus (Note - this is the page for the ECAMPUS version of BB 350.

BB 350 Oregon State University

The CLASSROOM version is different and should not be used by CLASSROOM students, nor should the ECAMPUS version be used by CLASSROOM students) The syllabus is required reading in this course. Download it HERE. If you would like a free biochemistry book called Biochemistry Free and Easy (BFE below), you may download it HERE. Technical Notes - You should use the YouTube videos for viewing and the iTunes U videos for downloading. You connect with iTunes U for OSU HERE. There are many songs sung on the lecture videos. This page has been replaced by a more recent version.


Programming. Source Code for Biology and Medicine. Tools. A question and answer site for bioinformatics. Online Lectures on Bioinformatics. - Canadian Bioinformatics Workshops (CBW) MCL - a cluster algorithm for graphs.