Biomarkers and Personalized Medicine A Review of Bioinformatics Blogs « Homologus Homolog.us blog is written by professional janitors dedicated to clean up US science. During lunch breaks and other time off from the job, we discuss bioinformatics. The name 'homolog.us' is not a spelling mistake, but is derived by taking Arabic translation of the 'O' in the original word. Please follow us on twitter – @homolog_us. To stay up to date with our commentaries, please follow us on twitter here Today we are reviewing and cleaning up the blog links at the right sidebar. The following three blogs are the ones most visited by us. Living in an Ivory Basement It is a blog maintained by Titus Brown, a Professor from Michigan State University. Why do we say so? The blog is updated once a week, but many updates have enough value to keep you thinking for weeks. NGS – Stuart Brown The blog is maintained by Stuart Brown, an Associate Professor at NYU School of Medicine. RNA-seq Blog This blog provides daily updates on published algorithms and research results related to RNA-seq. Openhelix
Life Sciences & Mathematics & Physical Sciences | Bioinformatics | Next Generation Sequencing Next-generation sequencing technologies are revolutionising genomics and their effects are becoming increasingly widespread. Many tools and algorithms relevant to next-generation sequencing applications have been published in Bioinformatics, and so to celebrate this contribution we have gathered these together in this 'Bioinformatics for Next Generation Sequencing' virtual issue. This will be a living resource that we will continually update to include the very latest papers in this area to help researchers keep abreast of the latest developments. Review: Harnessing virtual machines to simplify next-generation DNA sequencing analysisJulie Nocq et al. Bioinformatics (2013) 29 (17): 2075-2083 doi:10.1093/bioinformatics/btt352 Full Text Editorial -Bioinformatics for Next Generation Sequencing Alex Bateman and John QuackenbushBioinformatics (2009) 25: 429 Full Text Alignment Optimal spliced alignments of short sequence readsFabio De Bona et al.Bioinformatics (2008) 24: i174-80 Full Text ZOOM!
Top Bioinformatics Contributions of 2012 « Homologus Homolog.us blog is written by professional janitors dedicated to clean up US science. During lunch breaks and other time off from the job, we discuss bioinformatics. The name 'homolog.us' is not a spelling mistake, but is derived by taking Arabic translation of the 'O' in the original word. Please follow us on twitter – @homolog_us. Dear readers, two weeks back we asked for your suggestions for best bioinformatics innovations of 2012. In addition to topics covered in our blog over the entire year, we received several other good suggestions by email and in the comment section. That was lot of work, but then we faced the dilemma of how to judge between topics as diverse as a very good alignment algorithm and an excellent educational resource in bioinformatics. Please feel free to discuss in the comment section, if you do not agree with our choices or would like to suggest other interesting contributions missed by us. Best blog + Twitter feed – Getting Genetics Done + @genetics_blog 1. 2.
OpenHelix Blog us ENCODE leaders published their latest propaganda piece in PNAS - “Defining functional DNA elements in the human genome” and Dan Graur has done fantastic work of tearing it apart. @ENCODE_NIH in PNAS 2014: In 2012, the Dog Ate Our Lab Notebook and We Had No Laxative to Retrieve It Instead of rewriting his blog post, let us comment on random samples from here and there in the article. —————————————————————Marketing Your Science, LLC We never had honor of writing papers with co-authors from ‘scientific’ organizations like above. That leads to the questions of how much of the PNAS paper is science and how much is ‘advertising’ (i.e. half truths and systematic efforts to hide the negatives)? —————————————————————Proposed Future plan In the last paragraph, ENCODE tells us what their next ‘big science’ scheme is going to be. The data identify very large numbers of sequence elements of differing sizes and signal strengths. That is downright scary !! On Functional Elements ENCODE clowns wrote - Q1.
RHIPE: An Interface Between Hadoop and R for Large and Complex Data Analysis | LectureMaker, LLC Ron Fredericks writes: Dr. 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:
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). 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. 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 A package for drawing Bode, Nichols-Black and Nyquist diagrams. CircuiTikz for drawing electrical networks A set of LaTeX macros designed to make it easy to draw electrical networks in scientific publications. Pgfplots Provides a friendly and well documented interface for creating plots with normal or logarithmic scaling. Schéma-blocs avec PGF/TIKZ A set of macros for drawing block diagrams. bclogo A package for creating of colorful boxes with a title and logo. prerex A package for producing charts of course nodes linked by arrows representing pre- and co-requisites, and prerex, an interactive program for creating and editing chart descriptions. sparklines A simple package for drawing sparklines tikz-qtree: Simple syntax and smarter layout for trees tikz-timing tkz-berge Dia
Mathematics part 2 - Getting to grips with LaTeX by Andrew Roberts This tutorial builds on the basic foundations presented in the previous tutorial. 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 Looking better.
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