java -mx512m -jar BamView.jar

and extra command line options are given when '-h' is used:

java -jar BamView.jar -h

BAM files can be specified on the command line with the '-a' option:

java -mx512m -jar BamView.jar -a pathToFile/sorted.bam

If a BAM filename is not given on the command line BamView will prompt for a file to be entered. The BAM index file should have the same name as the BAM file but with a '.bai' suffix. Multiple BAM files can be loaded and overlaid in the viewer. To make this easier BamView will read in files that contain a list of filenames.

Address of the bookmark: http://bamview.sourceforge.net/

Bose Institute, Kolkata, invites applications from Indian Citizens for ONE (01) temporary position of Junior Research Fellow in the DBT sponsored project entitled, “Centre of Excellance (CoE) in Bioinformatics at Bose Institute”, running under Prof. Pinakpani Chakrabarti, Project Co-ordinatior, Bioinformatics Centre. The project is tenable upto 31.03.2017, but duration of the fellowship is one year only. The JRF will work with one of the faculty members of the center based on his / her motivation in any specific area on Bioinformatics.

Essential Qualification: 1st class M.Sc. / M.Tech degree in any stream of Chemical/ Biological Sciences with CSIR-UGC-NET-JRF / ICMR-JRF / DBT-JRF or CSIR-UGCNET- LS / GATE qualification.

Desirable qualification:

(i) Specialized knowledge in Organic / Physical chemistry.
(ii) Any exposure to research involving the small molecules (like drug) and / or protein structure determination or prediction.
(iii) Basic knowledge in computer programming, e.g. using FORTRAN, C, shell, perl etc.
(iv) Hands-on-experience on any of the following software : CHARMM/AMBER/NAMD/GROMACS,Gaussian/Gamess, Haddock/Autodock, Schrodinger etc. (or any other software serving similar purposes in molecular modeling)

Fellowship :

(i) Rs. 16,000/- p.m., plus admissible HRA & Medical Benefit for M.Sc. with CSIRUGC NET-JRF/ICMR-JRF/DBT-JRF or M.Tech. with CSIR-UGC NETJRF/
ICMR-JRF/DBT-JRF/CSIR-UGC NET-LS/GATE
(ii) Rs. 12,000/- p.m., plus admissible HRA & Medical Benefit for M.Sc. with CSIRUGC NET-LS/GATE

Age : Below 28 years as on the day on which the application is made (relaxable in case of SC/ST/OBC/WOMEN candidates only as per rule).

Interested and eligible candidates should apply on plain paper duly signed by them clearly mentioning the area of interest in research, possession of any desirable qualification (s) as mentioned above and quoting Advertisement No. on the envelop as well as application with complete Bio-data giving e-mail ID, Phone No. and details of qualification i.e. examination passed, year, division, percentage of marks, from Secondary onwards with attested copies of testimonials, addressed to the Registrar, Bose Institute, P-1/12, CIT Scheme VII-M, Kankurgachi, Kolkata-700054 on or before April 25, 2014.

The shortlisted candidates will be called for an interview. Applicants are advised to check our website for future updates.

Advertisement: www.boseinst.ernet.in/ADVT/14/p_2.pdf

The fate of a cell is ultimately the product of the regulation of its genes. Gene regulation is a coordinated process acting at multiple levels of which transcription and translation are the most prominent. The Valen group is dedicated to the fundamental question of how transcription and translation is integrated to obtain the desired protein abundance. The recent development of high-throughput next generation sequencing techniques to monitor both active translation and transcription has made it possible to study this connection at the genome scale.

This project aims to elucidate the links between regulation of translation and transcription. The applicant will analyze next generation sequencing data and model gene regulation on a genome-wide level to identify the features that affect the translational output of transcripts. The work will be done in close collaboration with experimental scientists who will test the predictions of the computational models.

Additional information on the position can be obtained by contacting Eivind Valen (eivind.valen@ii.uib.no).

The research fellow must take part in the University’s approved PhD program leading to the degree within a time limit of 3 years. Application for admission to the PhD program, including a project plan outline for the training module, will be worked out in collaboration with the research group in question.

In total, the fellowship period is 4 years, 25 % of this will be allocated to teaching and/or administrative duties. The fellowship period may be reduced if the successful applicant has held previous employment as a research fellow or similar.

http://www.jobbnorge.no/en/available-jobs/job/102235/research-fellow-phd-candidate-in-computational-biology-2-positions

Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer'

Abstract

Whole exome DNA sequencing (WES) or whole genome DNA sequencing (WGS) allows detection of mutations and polymorphisms in all exonic and genomic regions, respectively, while messenger RNA sequencing (RNA-Seq) enables quantitative analysis of gene expression. Mutations in the genome result in diverse transcriptional aberrations that can be missed in a stand-alone WES/WGS analysis. An integration of DNA variant analysis and RNA-Seq analysis enables one to investigate the consequences of genomic changes in the RNA transcripts including germline and somatic changes, imprinting, RNA editing and allele specific expression (ASE). In this webinar, we will demonstrate this integrated approach using Strand NGS to identify high confidence mutations, RNA editing events and ASE in cancer.

Webinar Details

Register here: http://www.strand-ngs.com/webinar_registration

About Speaker:

Dr. Veena Hedatale, has a PhD in Plant Genetics from The Radboud University, Netherlands focused on meiosis and recombination. Her prior academic experience at Cornell University was on genetic mapping and gene transformation in Rice. She has worked with Monsanto, and contributed to data mining, database development as well as gene/promoter/pathway discovery for traits related to yield and stress in crop species. At Strand, Veena has worked on Pharmacogenomic analysis of targets and Gene family analysis projects. Currently, she is part of the Strand NGS Application Science team and is involved in the analysis of next generation sequencing data.

Please feel free to contact us 24/5, for availing free online training or if you have any questions.

1. Make friends with local bioinformatics groups
2. Talk to your computing group
3. Obtain clear expectations
4. Rewrite your job description
5. Papers
6. Attend bioinformatics meetings
7. Try first, ask later

Address of the bookmark: http://biomickwatson.wordpress.com/2013/04/23/a-guide-for-the-lonely-bioinformatician/

Address of the bookmark: https://bernatgel.github.io/karyoploter_tutorial/

Address of the bookmark: https://github.com/AlexeyG/GRASS

Webpage : https://www.scilifelab.se/about-us/
Opportunity: https://www.scilifelab.se/about-us/career/