BOL: Related items

Following the scientific literature: A personal practical guide for young computational biologists

Rahul Agarwal — Fri, 23 Aug 2013 07:18:51 -0500

The goal of this guide is to describe why, when, where and how can you follow the most up-to-date science of interest and what papers/journals you should follow. The guide is biased towards the fields of genomics/systems biology.(from article)

Source: Igor Ulitsky & Ron Shamir

Address of the bookmark: http://acgt.cs.tau.ac.il/guides/LiteratureGuide.htm

The Institute for Molecular Bioscience (IMB), Bailey Lab

Sun, 14 Jul 2013 11:53:08 -0500

Pattern recognition and computational biology

MEME Suite software development; gene expression; mathematical modelling; gene regulation and transcription

Specialization:
Pattern recognition and modelling in computational biology

Link @ http://www.imb.uq.edu.au/tim-bailey

The Breitbart lab

Tue, 17 Sep 2013 18:19:49 -0500

Breitbart’s lab has created a new branch of biology called metagenomics in which one can sample and sequence genetic material collected from the environment.

Breitbart lab is located in the College of Marine Science at the University of South Florida. She is chosen as top "10 Brilliant" scientist by Popular Science magazine.
http://www.popsci.com/science/article/2013-09/mya-breitbart

Lab Link:
https://sites.google.com/site/breitbartgenomicslab/
http://www.marine.usf.edu/faculty/mya-breitbart.shtml

The Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM)

Sun, 14 Jul 2013 12:31:38 -0500

The Centre for Bioinformatics, Biomarker Discovery and Information-Based Medicine (CIBM) is committed to shortening the process of obtaining novel discoveries to achieve distinctively better outcomes in clinical practice and translational individualised medicine.

Link @ http://www.newcastle.edu.au/research-and-innovation/centre/cibm/about-us

Rehmsmeier group

Sat, 09 Nov 2013 20:07:07 -0600

"Our research focuses on understanding development, gene regulation, and epigenetics on a genome-wide scale, in the context of evolution. This involves the design and application of algorithms, statistics, and experimental approaches."

http://www.bccs.uni.no/units/cbu/research/rehmsmeier/

BioRuby :Ruby packages for biologist

Jitendra Narayan — Mon, 15 Jul 2013 01:36:28 -0500

BioRuby is a package of Open Source Ruby code, with classes for DNA and protein sequence analysis, alignment, database parsing, and other Bioinformatics tools.
BioRuby project provides an integrated environment in bioinformatics for the Ruby language. This project is supported by University of Tokyo (Human Genome Center), Kyoto University(Bioinformatics Center) and the Open Bio Foundation. The project was supported by Information-technology Promotion Agency (IPA) as an Exploratory Software Project in 2005
RubyForge is a home for open source Ruby projects: RubyForge is a home for open source Ruby projects. BioRuby project was started in late 2000, and is still in progress. Currently, there are over 80 files and 15,000 lines (except comment-only lines) in our source code. This might be equivalent to twice or more lines of other languages because of Ruby's extremely high descriptive power.

Classes for
Multiple alignment (Bio::Alignment),
Gene Ontology(Bio::GO),
PDB (Bio::PDB),
FANTOM database(Bio::FANTOM),
GFF (Bio::GFF) and KEGG
Orthology (Bio::KEGG::KO).

They also added support for many applications such as PSORT, SOSUI, TargetP, TMHMM, GenScan, ClustalW, MAFFT, and KEGG API.

Wiki Links
http://bioruby.open-bio.org/wiki/BioRubyOnRails
http://dev.bioruby.org/en/

BioRuby in Anger
http://dev.bioruby.org/en/?BioRuby+in+Anger

BioRuby RDocs
http://bioruby.org/rdoc/

BioRuby Tutorial Website
http://dev.bioruby.org/en/?Tutorial.rd

Why BioRuby Hub for BioRuby
http://www.linuxjournal.com/article/5915

Social Coding Hub for BioRuby
http://www.linuxjournal.com/article/5915

Bioinformatics on Rails: BioRuby Tutorial
http://bioinforuby.blogspot.com/2008/02/bioruby-tutorial.html

RRA BioRuby
http://raa.ruby-lang.org/project/bioruby/

BioRuby Project Discussion Group
http://portal.open-bio.org/mailman/listinfo/bioruby

BioRuby related Projects: Project tree
http://rubyforge.org/softwaremap/trove_list.php?form_cat=252

Reference
http://www.jsbi.org/journal/GIW03/GIW03P191.pdf

Application Scientist in Strand LifeSciences Bangalore

Mon, 07 Apr 2014 08:17:32 -0500

Job Description
We are looking for a motivated application scientist to help evaluate, compare, and develop next generation sequencing (NGS) data analysis methods. The successful candidate should be able to quickly understand the state-of-art computational biology techniques, prototype them and perform benchmarking studies. The candidate must also be comfortable working with people from different disciplines and be able to present data analysis results in a clear and effective manner. The candidate is also expected to interact with customers as needed, write technical reports and publish new methods and/or data analysis findings in public forums.

Candidate Requirements:
A PhD in computer science, computational biology, Bioinformatics, or a related field, along with sufficient programming skills for prototyping. Experience with next generation sequencing data analysis is required. Candidates with MS degree but with relevant work experience can also be considered.

To Apply
To apply, please send your updated CV and cover letter to Dr. Rohit Gupta (rohit@strandls.com).

Source: http://www.strandls.com/application-scientist

Postdoctoral position in bioinformatics @ Sweden

Sun, 14 Jul 2013 13:49:57 -0500

Information about the department
The Department of Mathematical Sciences at Chalmers University of Technology and the University of Gothenburg has about 170 faculty and staff and is the largest department of mathematical sciences in the Nordic countries. The department belongs to both Chalmers University of Technology and the University of Gothenburg (for more information see http://www.chalmers.se/math/).

Job description
We are looking for a motivated, self-driven post-doctoral researcher to work with large-scale sequence data analysis. The position is for 24 months and located at Mathematical Statistics, Department of Mathematical Sciences in Erik Kristiansson’s research group. We are focused on methods development for and analysis of next generation DNA sequencing, in particular comparative metagenomics and gene expression analysis (RNA-seq). We have strong interdisciplinary profile and are actively collaborating with several experimental groups, especially within the environmental sciences, ecology, infectious diseases and cancer genomics. More information is available at http://bioinformatics.math.chalmers.se.

The Post-doctoral position is an appointment that offers an opportunity to qualify for further research positions within academia or industry. The majority of your working time is devoted to your own research, normally as a member of a research group. Included in your work is also to take part in supervision of Ph.D. students and M.Sc thesis students. Teaching of undergraduate students may also be included to a small extent.

The employment is limited to a maximum of 2 years (1+1).

Qualifications
The applicant should have Ph.D. degree preferably in bioinformatics, mathematics, statistics, computer science or equivalent by the start of the appointment. Experience from analysis of large-scale data, in particular from next generation DNA sequencing, is highly valued. The applicant should also be proficient in programming (e.g. Python/Java/C) and comfortable with Unix/Linux systems. Interaction with experimental biologists is central and good collaborative skills are therefore important. Fluency in written and spoken English is a strong requirement. As a post-doctoral researcher you are expected to work independently and to be able to supervise/co-supervise PhD and Master’s students.

Application procedure
The application should be marked with Ref 20130126 and written in English. The application should be sent electronically via Chalmers webpage.

Application deadline: September 8, 2013.

For questions, please contact:
Ass prof. Erik Kristiansson, Matematiska Vetenskaper, erik.kristiansson@chalmers.se, +46 31-772 3521, +46 70-5259751.

Chalmers continuously strive to be an attractive employer. Equality and diversity are substantial foundations in all activities at Chalmers.

Bioinformatician for a lab at the Weizmann Institute of Science, Israel

Mon, 13 Oct 2014 04:38:28 -0500

We are looking for enthusiastic, motivated and talented people, at all career stages (MSc, PhD, postdoctoral fellows), to join the lab! Bioinformatics in particular are invited to apply.
Our lab focuses on understanding molecular mechanisms of protein modifications in cancer and immune regulation.
We employ advanced high-throughput proteomic and genomic methods, cell biology, biochemistry, immunology, in-vivo models as well as systems biology and bioinformatics to study the biology of PTMs in health and disease. Read more here: http://yifatmerbl.com.

STUDENTSHIP and TRAINEESHIP @ University of Madras

Sat, 16 Nov 2013 19:27:40 -0600

Bioinformatics Infrastructure Facility
University of Madras
Chennai 600 025

Applications are invited for the STUDENTSHIP and TRAINEESHIP vacancies to carry out project/research work in the DBT - Bioinformatics Infrastructure Facility with consolidated stipend of Rs.5,000/- per month.

Essential Qualification

Student Trainee: Those who have completed M.Sc., Bioinformatics/Biophysics/Life sciences or Pursuing M.Tech., Bioinformatics/Biotechnology

Duration : 3-4 Months

Student Trainee: Those who are pursuing M.Sc Bioinformatics/Biophysics/ Life sciences/others

Duration : 2-3 Months

Mail your CV on or before 25th November 2013 to shirai2011@gmail.com and hard copy to "Dr. D. Velmurugan, Professor & Head, CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025". Also, the applicants are requested to attend the interview on 29th November, 2013 at 11 A.M.

www.unom.ac.in/uploads/announcements/bifadvertisement_20131114080003_23240.pdf