BOL: Related items

Arvados

Martin Jones — Sat, 20 Sep 2014 16:54:21 -0500

Arvados is a free and open source bioinformatics platform for genomic and biomedical data. User can Store | Organize | Compute | Share the data for free.

Address of the bookmark: https://arvados.org/

Nieduszynski Group

Fri, 26 Sep 2014 19:35:06 -0500

Complete, accurate replication of the genome is essential for life. All chromosomes in eukaryotic cells must be duplicated and then segregated to daughter cells to ensure genetic integrity and produce the large number of cells that make up a multicellular organism. We are using genetic, genomic and computational methods to understand how chromosome replication is regulated to ensure genome stability. By focusing on the basic biology that underpins cell growth and division we aim to provide new insights that may help our understanding of diseases such as cancer and congenital disorders.

More http://www.nieduszynski.org/index.php
http://www.path.ox.ac.uk/research/cell-biology-and-pathology/conrad-nieduszynski-group

Big genomic data on Google Cloud Platform

Fri, 17 Oct 2014 02:16:00 -0500

As the cost of DNA sequencing has dropped, the volume of data produced has risen into the petabytes. Google is working with the genomics community to define a standard API for working with big genomic data sets in the cloud. Building on Google Cloud Platform, we show how to store, process, explore and share genomic data using technologies like BigQuery, AppEngine MapReduce, R and more.

translate2R

Rahul Nayak — Fri, 21 Nov 2014 01:16:06 -0600

After their presentation at the international “user!” conference, data analysis specialist eoda starts the public alpha testing of translate2R. With the start of alpha testing the innovative migration solution by the company hailing from Kassel discards the working title “translateR” and takes on the final product brand name “translate2R”. translate2R is a service for the automated translation of SPSS® syntax to R code, therefore supporting data analysts with a quick and low-risk migration to R.

The manual translation of many, frequently rather complex SPSS scripts often presents itself as a tedious and error-prone task, and represents a rather large obstacle for many analysts and companies to migrate to a modern, open source data management and analysis tool like R. With translate2R this hurdle will be diminished substantially.

Find at https://service.eoda.de/translater/?lang=en

irishgrid: Irish Grid Mapping System

Jit — Fri, 26 Dec 2014 07:53:24 -0600

Perl module for creating geographic 10km-square maps using either SVG or PNG (with GD library) output format.

Originally design to map the location of objects in a 10 km map IrishGrid includes:

native support of the Irish Grid System (see http://www.osi.ie/)
optimize for speed (there's as less as possible data to conversion)
customized color functions

https://code.google.com/p/irishgrid/downloads/detail?name=irishgrid.pl

Address of the bookmark: https://code.google.com/p/irishgrid/

Zhang Lab

Sun, 28 Dec 2014 12:43:08 -0600

We develop and use integrative bioinformatics approaches to extract biological meanings from experimental data and generate hypotheses for experimental validation. Please explore our website to learn more about our people and our research.

More at http://bioinfo.vanderbilt.edu/zhanglab/

Linux operating system aimed at scientists

Pranjali Yadav — Mon, 19 Jan 2015 08:30:49 -0600

The Bio-Linux operating system is based on Ubuntu 14.04 LTS (Trusty Tahr), and the previous version was using Ubuntu 12.04 LTS. The developers only use LTS releases and that means that upgrades for this distro don't come along all that often.

This Linux distribution is aimed at scientists and it comes with more than 250 bioinformatics packages, 50 graphical applications and several hundred command line tools. And this is just skimming the surface of what the OS can do. Users have access to even more apps from the official repositories.

Bio-Linux is using an Ubuntu LTS version as its base

The fact that it uses Ubuntu LTS versions for the base is a good thing because it means its users won't have to worry about the support. Ubuntu 14.04 LTS is supported until 2019, so people who are using Bio-Linux shouldn't have a problem.

"An updated Bio-Linux 8 version is now on the website in ISO and OVA versions. As usual, there is no need to download this version if you are an existing user. All updates to existing packages will be applied to your system through the update manager and new packages are all available via apt-get or Synaptic," reads the announcement.

The changelog also states that a problem that was preventing the desktop to not start on VirtualBox has been fixed, the QIIME and Bowtie-Bio tools have been upgraded, the pandaseq paired end assembler has been added, and the beginners tutorial specific to Bio-Linux 8 has been improved.

Check out the official announcement for a complete list of changes and updates. You can download Bio-Linux 8.0.5 right now from Softpedia and give it a spin. It has the Unity desktop and now it runs very well in virtual environments.

Reference @ http://news.softpedia.com/news/Bioinformatics-Distro-Bio-Linux-8-0-5-Now-Available-for-Download-469867.shtml

JRF/RA Structural/Computational Biology at ICGEB

Thu, 29 Jan 2015 11:52:40 -0600

Research Associate and JRF positions in the Structural and Computational Biology Group starting 1st March 2015. Collaborative projects include work on:

a) bioinformatics, systems and computational biology
b) malaria
c) drug discovery
d) genomics
e) microbiology
f) metabolic disorders
g) molecular medicine

Eligibility: Applicants must have one of the following :

1) INSPIRE award for undertakig either PhD or Postdoctoral research;
2) SPM award for PhD;
3) JRF for pursuing PhD from CSIR/DBT/ICMR

Interest and experience in Biochemistry/Bioinformatics/Biophysics/ Chemistry/Genomics/Molecular Biology/ is essential.

Submit curriculum vitae to sb.icgeb@gmail.com by 20 February 2015

RA / Research Associate Bioinformatics/Computational Biologist

Thu, 26 Feb 2015 03:44:24 -0600

The following posts are urgently required to be filled for the Department of Biotechnology, Government of India funded project entitled "Computational Core for Plant Metabolomics" administrated by Prof Indira Ghosh, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110 067

RA / Research Associate (Bioinformatics/Computational Biologist)
Salary: Rs. 23000/- + HRA
Vacancy: 1
Essential Qualifications: PhD, preferably in plant biotechnology/biochemistry/Bioinformatics with experience in analyzing high throughput omics-based data. Desired Skills: Prior experience in handling and guiding bioinformatics, metabolomics data, managing the project portal, preparing and filing reports etc. Will be expected to communicate with user groups and coordinate with LIMS group in Hyderabad and the Cheminformatics group in Delhi.

Address: Prof Indira Ghosh, room #12 Project Investigator, (Core Metabolomics) School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110 067.

Apply Details
Last Date: March 3rd 2015
Web/Notification URL http://www.jnu.ac.in/Career/currentjobs. htm

R for Microsoft Excel

Jitendra Narayan — Wed, 18 Feb 2015 00:43:27 -0600

If you currently use a spreadsheet like Microsoft Excel for data analysis, you might be interested in taking a look at this tutorial on how to transition from Excel to R by Tony Ojeda. The tutorial explains how to use R functions in place of Excel formulas, including tools like =AVERAGE and =VLOOKUP. For the most part, it uses modern R packages to keep the R code clear and concise.

You'll likely still be using Excel as a data source, though, so you'll also want to check out this guide to importing data from Excel to R from MilanoR.

Reference http://www.r-bloggers.com/an-r-tutorial-for-microsoft-excel-users/