BOL: Related items

OpenCPU

Rahul Nayak — Sun, 05 Jul 2015 18:34:46 -0500

OpenCPU is a system for embedded scientific computing and reproducible research. The OpenCPU server provides a reliable and interoperable HTTP API for data analysis based on R.

The OpenCPU JavaScript client library provides the most seamless integration of R and JavaScript available today.

OpenCPU uses standard R packaging to develop, ship and deploy web applications. Several open source example apps are available from Github.

Installing your own OpenCPU server is super easy and only takes a few minutes.

More at https://www.opencpu.org/

SRF/JRF Bioinformatics at CIARI

Fri, 04 Dec 2015 00:10:09 -0600

Realizing the importance of Island Agriculture to meet the requirements of local population and tourists, Indian Council of Agricultural research (ICAR) established Central Island Agricultural Research Institute, Port Blair on June 23rd, 1978 by merging different regional research stations of ICAR institutes located in Islands. The ultimate aim of CIARI is the developments of island agricultural production technologies which utilizes the strengths of the island and convert the constraints in opportunities, without causing any ill effect to the fragile ecosystem of the island.The institute has made tremendous progress in the Agriculture development of the islands during the last three decades. Keeping in view the natural resources of the islands diversity, fragile ecosystem, research program would be designed to maximize the productivity without disturbing to the islands ecosystem to provide better and decent livelihood and as a source of revenue and resource generation. Research and development in Agriculture sector should cover all disciplines in order to have a balanced progress in all disciplines for the overall benefits of the farmers of these islands.

Position I

Job Title : Junior Research Fellow

No. of Posts : One

Project : Establishment of sub distributed information centre

Qualification : M.Sc in Basic Science with NET or B.Sc in professional course with NET or M.Sc in professional course

Desired Experience : Experience in Bioinformatics and molecular biology

Payscale : Rs. 25000 per month

Age Limit : Upto 35 for men and 40 for women with 5 years relaxation to SC/ST and 3 years relaxation for OBC.

Position II

Job Title : Traineeship

No. of Posts : One

Project : Establishment of sub distributed information centre

Qualification : B.Sc Bioinformatics /Biotechnology / Life Science / Computer Science

Desired Experience : Experience in Bioinformatics and molecular biology

Payscale : Rs. 8000 per month

Age Limit : Upto 35 for men and 40 for women with 5 years relaxation to SC/ST and 3 years relaxation for OBC.

Position III

Job Title : Studentship

No. of Posts : Two

Project : Establishment of sub distributed information centre

Qualification : B.Sc Bioinformatics /Biotechnology / Life Science / Computer Science

Desired Experience : Experience in Bioinformatics and molecular biology

Payscale : Rs. 8000 per month

Age Limit : Upto 35 for men and 40 for women with 5 years relaxation to SC/ST and 3 years relaxation for OBC.

How to Apply : Candidates who meet the requirements can attend the walk in interview at CIARI,Port Blair on 09.12.2015 10.30AM.

http://icar-ciari.res.in/employment/9-12-15.pdf

Post-doc position at LABGeM - Evry, France

Fri, 11 Dec 2015 06:24:00 -0600

The LABGeM team (CEA/Genoscope, CNRS UMR 8030, France, Dir. Claudine Médigue) is developing integrated approaches which combines bioinformatics methods based (i) on genomic and metabolic contexts, (ii) on an orignal metabolic network representation and (iii) on a structural classification of active sites for the discovery of new metabolic enzymatic activities.

We are hiring a post-doctoral fellow for the development of innovative bioinformatics methods to explore metabolic networks and enzyme families. These methods will be based on protein family analysis and graph approaches combining genomic and metabolic contexts.

For more details, please see this link : http://goo.gl/tHQOqk

Qualifications:
PhD degree in bioinformatics or computational biology
- Previous experience in network or protein family analysis
- Programming skills (C/C++, Python, Java) and in common biostatistical analyses
- Team player, innovative and creative thinking, good oral and written communication skills

24 months, Post Doctoral position
Start: from March 2016
Place: CEA, Genoscope UMR8030, LABGeM (Laboratory of Bioinformatics Analyses for Genomics and Metabolism), Evry, France
Contact: David Vallenet, vallenet@genoscope.cns.fr
Publications: https://scholar.google.com/citations?user=rJNPLSAAAAAJ
Remuneration per month: from 2,850 €

Interested candidates should send their CV, statement of research interests, and contact information of at least 2 references to David Vallenet (vallenet@genoscope.cns.fr).

Microscope

Jitendra Narayan — Fri, 04 Mar 2016 05:26:31 -0600

Microscope Platform user documentation.

The MicroScope platform is available at this URL:

https://www.genoscope.cns.fr/agc/microscope

Address of the bookmark: http://microscope.readthedocs.org/en/latest/index.html

Project Assistant at IISER Mohali

Fri, 29 Jan 2016 11:04:27 -0600

Project Assistant Job position in Indian Institute of Science Education & Research (IISER) Mohali

Title : In silico understanding of molecular basis of recognition, binding, and regulation of mRNA by STAR family of transcriptional regulators.

No. of Post : 01

Department : Science and Technology

Qualifications : M.Sc./B.Tech in computational life sciences, computational chemistry, computational natural sciences or allied areas. Working experience in MD simulations, bioinformatics, molecular modeling, and drug designing is desirable and plus

Emoluments : As per DST norms
How to apply

Applicants are requested to send application along with bio-data and a summary of previous projects (if any) as a PDF file with the e-mail to Dr. Monika Sharma, Email: mnsharma@iisermohali.ac.in. Last date of applications is 17:00 IST. Feb 15, 2016. Shortlisted candidates will be called for interview on Feb 22, 2016.

More at http://14.139.227.202/tenders/tenderinvite/index.php/iiserm-project-openings/554-applications-are-invited-to-work-as-project-assistant-in-a-dst-inspire-research-project-funded-by-department-of-science-and-technology-india

RATT

Jitendra Narayan — Sun, 07 Feb 2016 16:09:40 -0600

RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome.

It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between strains and even different species, like Plasmodium chabaudi onto P. berghei, between different Leishmania species or Salmonella enterica onto other Salmonella serotypes. RATT is able to transfer any entries present on a reference sequence, such as the systematic id or an annotator's notes; such information would be lost in a de novo annotation.

More at http://ratt.sourceforge.net/

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

Pilon

Rahul Nayak — Mon, 08 Feb 2016 15:56:18 -0600

Pilon is a software tool which can be used to:

Automatically improve draft assemblies
Find variation among strains, including large event detection

Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:

Single base differences
Small indels
Larger indel or block substitution events
Gap filling
Identification of local misassemblies, including optional opening of new gaps

More at https://github.com/broadinstitute/pilon/wiki

Address of the bookmark: https://github.com/broadinstitute/pilon/wiki

Advanced Bash-Scripting Guide

Jit — Thu, 18 Feb 2016 04:50:51 -0600

This tutorial assumes no previous knowledge of scripting or programming, yet progresses rapidly toward an intermediate/advanced level of instruction . . . all the while sneaking in little nuggets of UNIX® wisdom and lore. It serves as a textbook, a manual for self-study, and as a reference and source of knowledge on shell scripting techniques. The exercises and heavily-commented examples invite active reader participation, under the premise that the only way to really learn scripting is to write scripts.

This book is suitable for classroom use as a general introduction to programming concepts.

More at http://tldp.org/LDP/abs/html/

Address of the bookmark: http://tldp.org/LDP/abs/html/

svelter

Jitendra Prajapati — Mon, 29 Feb 2016 17:33:15 -0600

This software is designed to identify both simple and complex rearrangements from paired-end sequencing data. Users could ran it easily by just alling SVelter.py with proper parameters. It's also possible to ran it on multiple cores by calling different sub-functions separately.

More at https://github.com/mills-lab/svelter/

Address of the bookmark: https://github.com/mills-lab/svelter/

QUAST: quality assessment tool for genome assemblies

Jitendra Prajapati — Wed, 06 Apr 2016 18:23:33 -0500

QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.
It can works both with and without a given reference genome.
The tool accepts multiple assemblies, thus is suitable for comparison.

More at http://bioinf.spbau.ru/quast

http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long