BOL: Related items

RA at Central University of Rajasthan

Tue, 09 Feb 2016 03:53:35 -0600

Research Fellow Bioinformatics

Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech)

Location : Ajmer

Last Date : 13 Feb 2016

Hiring Process : Face to Face Interview
Central University of Rajasthan

Research Fellow Job vacancies in Central University of Rajasthan

Project Title : “Development of natural product derived febrifugine ananlogues as a novel therapeutics against visceral leishmaniasis”

No. of Post : 01

Qualification : Master of Biochemistry, Biotechnology, Bioinformatics and related biological sciences with minimum 55%, Age limit as per government rule.

Desirable Experience : Candidates with experience in cell culture, Chemoinformatics, and Parasitology will be preferred.

Fellowship : Rs. 25,000/- p.m. consolidated for NET qualified (14,000/- p.m. consolidated for Non-NET)
How to apply

The candidates may apply on a plain paper, along with their curriculum vitae (including name, date of birth, academic qualification starting from 10th class, summary of research experience, email id, phone number and passport size photograph) and email to vkprajapati@curaj.ac.in or post the hard copy to the Dr. Vijay Kumar Prajapati PI, DST-SERB Project (YSS/2015/000716), Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Dist- Ajmer, Rajasthan, 305 817 on or before 13th February 2016.

More at http://www.curaj.ac.in/Default.aspx?PageId=241

NCBI Remap

Jit — Thu, 11 Feb 2016 11:02:26 -0600

NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap.

More at http://www.ncbi.nlm.nih.gov/genome/tools/remap

API http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api

Address of the bookmark: http://www.ncbi.nlm.nih.gov/genome/tools/remap

Przeworski lab

Mon, 15 Feb 2016 05:41:54 -0600

Genetic differences among individuals reflect the combined effects of mutation, recombination, population history and natural selection. As a result, studies of natural variation can provide important insights into evolutionary and genetic mechanisms: as examples, DNA sequence conservation among distantly related species can help identify functional roles too subtle to be detected in lab settings, while analyses of population variation allow for inferences about events that are too infrequent to be measured directly. Our research employs this general approach to learn about the dynamics of adaptation and the determinants of recombination and mutation, in humans and in other species.

More at http://przeworski.c2b2.columbia.edu/

BioToolbox

Jit — Fri, 19 Feb 2016 09:14:44 -0600

This is a collection of libraries and high-quality end-user scripts for bioinformatic analysis, including working with gene annotation, collecting data scores from a variety of modern file formats, and conversion between file formats. The Bio::ToolBox libraries provide a unified, abstracted interface to multiple common gene annotation formats and the collection of data from multiple data files. They rely on BioPerl SeqFeature libraries and related adaptors to access binary file formats including Bam, BigWig, BigBed, and USeq. The Bio::ToolBox package includes scripts for setting up databases of annotation, collecting annotated features, collecting genomic data relative to features, manipulating and analyzing data, and data format conversion.

More at http://cpansearch.perl.org/src/TJPARNELL/

Address of the bookmark: http://cpansearch.perl.org/src/TJPARNELL/

RA at ICAR - INDIAN INSTITUTE OF OILSEEDS RESEARCH

Mon, 22 Feb 2016 05:21:34 -0600

ICAR - INDIAN INSTITUTE OF OILSEEDS RESEARCH

HYDERABAD-500030

F.No. 5-42/2016/Rectt.

WALK IN INTERVIEW

Eligible candidates are invited to attend Walk in Interview to fill up the (purely) temporary post of Junior Research Fellow (One) under Extramural Research Project entitled “Transcriptome and proteome analysis for identification of candidate genes responsible for pistillate nature in castor “ to be held on 04.03.2016 at 11.00 AM at ICAR – Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad. The tenure of the project is up to 31.03.2017. The requirement and other terms and conditions for the Junior Research Fellow are as under :-

Junior Research Fellow (One)

Nucleic acid isolations, molecular analysis, bioinformatic analysis

.M.Sc.Biotechnology/Bioinformatics

Post Graduation in Life Sciences.

Candidates having Post Graduate degree in Basic Sciences with 3 years Bachelor’s degree and 2 years Master’s Degree 1,2,3 should have NET qualification.

Experience in Plant Biotechnology and Bioinformatics

Rs.25000/- + 30% HRA per month (At present)

More Info : http://icar-iior.org.in/media/docs/employment/2016/jrf-int.pdf

Scientist - Computational Genomics (Two Positions)

Sat, 12 Mar 2016 18:07:56 -0600

ICRISAT is a non-profit, non-political organization that conducts agricultural research for development in Asia and sub-Saharan Africa with a wide array of partners throughout the world. Covering 6.5 million square kilometers of land in 55 countries, the semi-arid tropics is home to over 2 billion people, with 650 million of these being the poorest of the poor. ICRISAT and its partners help empower those living in the semi-arid tropics, especially smallholder farmers, to overcome poverty, hunger, malnutrition and a degraded environment through more efficient and profitable agriculture.

ICRISAT is headquartered in Patancheru near Hyderabad, India, with two regional hubs and five country offices in sub-Saharan Africa. ICRISAT, established in 1972, is a member of the CGIAR Consortium. For more details, see www.icrisat.org.

Responsibilities:Design efficient SQL queries for pulling large sequencing projects.
Serve as a technical adviser to the project leadership and provide computational perspective on product design and deliverability.
Develop and oversee a rapid and incremental software development and release schedule.
Design the software architecture, oversee the implementation and evolution of the design on appropriate hardware platforms.
Working collaboratively in a team environment to design, code, test, debug, and document programs for an integrated genomic analysis pipeline in a rapid and incremental software development and release schedule.
Supervise and review code development and ensure that software products meet project objectives in terms of functionality, scalability, robustness and user experience.
Implement and oversee the QA/QC practices to ensure the development team is adhering to quality standards.
Work closely with the application specialist to integrate feedbacks from teams in each CGIAR center into software customization and improvement.
Assist in training of breeders in the CGIAR centers to use software developed.
Personal Profile:

The applicant should have:

Understanding of genomics data and advanced knowledge of Java, and C/C++ as the programming languages and any of the scripting language like perl and/or Python, SQL
High Performance Computing, data architecture, database platforms and QA/QC practices in software engineering.
She/he should have solid experience in software development projects, preferably as a senior programmer or in the software project management role, and in projects involving big data.
Excellent communication skills are needed to work in this multi-disciplinary, multi-location and multi-cultural team.
Ability to mentor colleagues in quality software development practices is desired.
Educational Qualification : Ph. D or Masters Degree in Computational Biology / Computational Genomics or Equivalent with Research Experience in Mentioned Areas.

More at http://www.icrisat.org/careers/

One-Year Internship In Computational Biology & Bioinformatics

Mon, 04 Apr 2016 05:35:57 -0500

This one-year internship program has an inter-disciplinary curriculum that rests on research strengths and infrastructure at the computational biology & bioinformatics facility at Rajiv Gandhi Centre for Biotechnology . Using live demonstration platforms of high end genomic analysis systems including next generation sequencing, advanced proteomics platforms, advanced bio-imaging, student seminars in addition to computer laboratory based courses, interns will get state of the art exposure and training in application of bioinformatics to biomedical research.The internship involves 8 months of hands on training in wet and dry laboratory methods and a four-month dissertation. This internship program is designed for students who would like to gain good knowledge and experience in Bioinformatics as a prelude to taking up a PhD course or look for employment opportunities. The subjects covered during the internship will include but not limited to:
• Systems Biology
• Genomic Informatics
• Proteomic Informatics
• Biomedical Text Mining
• Ontologies
• Data Integration
• Data Mining
• Protein Structure & Function
• Metabolomics
• Molecular Evolution
• Pathways & Networks
• Resource Development
• Scripting & Algorithms
Qualifications: Admission to the Internship requires a first class degree in Engineering Sciences (Biotechnology/Computer Science), Medical/Dental/Pharmaceutical Sciences (MBBS or BDS or BAM or B.Pharm) or a Masters degree in Life Science, Medical Laboratory Technology, Biotechnology, Bioinformatics or Computer Science.
Internship Fees: The internship fee for the 12-month program is Rupees 70,000 (Rupees Seventy thousand). This is payable as an initial admission fee of Rs. 10,000 followed by payments of Rs. 6,000 monthly from months 3 to 9. The final completion certificate will be given after payment of all fees.
Mode of Selection: Selection will be based on interview and the top 5 candidates will be shortlisted for the program.
Location: Thiruvananthapuram

More at http://rgcb.res.in/TrainingPrograms/internship.php

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

Jit — Wed, 06 Apr 2016 13:27:23 -0500

PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.

More at http://www.exelixis-lab.org/web/software/pear

Paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933873/

Address of the bookmark: http://www.exelixis-lab.org/web/software/pear

Sr.Bioinformatics Analyst (NGS) @ OcimumBio

Mon, 02 May 2016 04:41:22 -0500

Sr.Bioinformatics Analyst (NGS)

Experience Required: 3-5 years of experience
No of Positions : Multiple
Qualifications: Candidates with minimum qualification as M.Sc Bioinformatics with 3-5 years of experience in Life sciences R&D or Pharma Industry.
Ph.D candidates with research experience in Bioinformatics with publications in International journal and minimum 2 years of industry experience in clinical genomics will be preferred for this position.

Requirement:

1. Must have basic understanding of molecular biology and Genomics.
2. Experience in application development or must have expertise in programming using either of Perl/Python.
3. Experience in statistical programming using R/Bioconductor/Matlab.
4. Strong concept in statistical and mathematical modelling.
5. Experience in designing and developing the bioinformatics pipeline.
6. Must have minimum 2+ years of hands on experience in NSG data analysis such as RNA-Seq,Exome-Seq ,Chip-Seq and downstream analysis.
7. Knowledge in WGS ,WES, Targeted re-sequencing,GWAS and population genomics will be preferred.
8. Must have experience working on opensource software/Framework and commercial software for NGS data analysis and reporting.
9. Should be aware of handling big data and guiding team members on multiple projects simultaneously.
More at http://www.ocimumbio.com/careers1/
10. Should have experience coordinating with different groups of clinical research scientist for various project requirements.
11. Ability to work as team as well as independently with minimal support.

Supposedly Educational R

Rahul Nayak — Tue, 03 May 2016 16:43:08 -0500

R 3.3.0 (codename “Supposedly Educational”) was released today. You can get the latest binaries version from here. (or the .tar.gz source code from here). The full list of new features and bug fixes is provided below.

If you are using Windows you can easily upgrade to the latest version of R using the installr package. Simply run the following code in Rgui:

install.packages("installr") # install 
setInternet2(TRUE)
installr::updateR() # updating R.

Running “updateR()” will detect if there is a new R version available, and if so it will download+install it (etc.). There is also a step by step tutorial (with screenshots) on how to upgrade R on Windows, using the installr package. If you only see the option to upgrade to an older version of R, then change your mirror or try again in a few hours (it usually take around 24 hours for all CRAN mirrors to get the latest version of R).

I try to keep the installr package updated and useful, so if you have any suggestions or remarks on the package – you are invited to open an issue in the github page.