BOL: Related items

JAMIA HAMDARD Bioinformatics Faculty Jobs 2014

Sat, 20 Sep 2014 21:00:05 -0500

JAMIA HAMDARD

(Deemed University)

Hamdard Nagar, New Delhi – 110 062

R E C R U I T M E N T

(Advertisement No. 5/2014)

Applications on prescribed form are invited for filling up the following teaching positions in the Department of Biotechnology, Faculty of Science in the university. Eligible candidates may apply on or before 30.09.2014.

1. Professor/Associate Professor - One in Pay Band of Rs. 37400-67000+ AGP Rs.10000/9000

2. Assistant Professor - Two in Pay Band of Rs. 15600-39100+ AGP Rs. 6000/-

ASSISTANT PROFESSOR – 02 (including 01 SFS)

Specialization : Bioinformatics

Qualification and Experience :

Ph.D. in Biotechnology or an allied discipline with M.Sc. in Biotechnology/ Biochemistry in the First division or equivalent grade from a recognized University/ Institute.

NET in Life Science or allied discipline in addition to the above qualification.

Experience : At least two years of Post-doctoral teaching and/or research experience in Bioinformatics or relevant field in a UGC recognized Institution of repute or international research institute/ University. Proof of research to be evidenced by publications in SCI-indexed journals of high impact factor as the first or corresponding author.

Note : University may consider exempting candidates from NET, who has been awarded Ph.D. degree from ‘A’ Grade accredited University following the procedure as notified by the UGC in its Regulations of 2009 and adopted by Jamia Hamdard.

For more information: http://www.jamiahamdard.ac.in/PDF/Online%20application%20form%20_Teaching_1.pdf
http://www.jamiahamdard.ac.in/PDF/PBAS.pdf

Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?

Strand — Tue, 04 Aug 2015 05:14:07 -0500

Will MinION Nanopore sequencing increase the number of Next Generation Sequencing projects?

Finishing !!

Jit — Sat, 20 May 2017 15:50:20 -0500

The process of finishing a genome and moving it from a draft stage (the result of sequencing and initial assembly) to a complete genome is typically a time and resource intensive task. The advent of new sequencing technologies has come with its own set of opportunities and pitfalls in the finishing process. While genomes can now be sequenced to high redundancy in a cost-effective manner, the process of assembling the genomes is more challenging and often draft genomes are fragmented into hundreds of contigs. Correspondingly, the task of producing the complete genome can involve months of lab work and thousands of finishing experiments and is usually done in large genome centers.

The work in our lab has focussed on computational approaches to speed-up the finishing process. Specifically, we have explored the use of optical mapping and mate-pair data to augment assemblies and direct finishing experiments. The tools developed in our lab have been used in several finishing projects, producing complete genomes (and near-complete ones) with surprisingly little computational and experimental effort (Nagarajan et al., in submission). The executables (as well as source code) for these tools are freely available here:

Scaffolding using Optical Restriction Mapping
Optical Maps are global, ordered maps of restriction site locations in a genome. This information can be quite useful in scaffolding contigs from a shotgun assembly to guide the finishing process. A set of programs to exploit optical maps for assembly can be found here: SOMA v2.0 (63 MB tar.gz file). This version of SOMA contains several improvements to programs in v1.0 as well as new scripts for working with multiple maps, contig graphs and scaffolds.
Augmenting assemblies with mate-pair data
Mate-pair information can be valuable in augmenting short-read assemblies and reconstructing the genome as larger scaffolds. AMOS-Hybrid is a pipeline written in the AMOS framework (open-source assembly tools) to merge arbitrary mated reads into an existing assembly and merge contigs and create scaffolds where possible. Source code and executables for AMOS-Hybrid are available here: AMOS-Hybrid v1.0 (142 MB tar.gz file).
Assembly and sequence-composition guided finishing
Contigs from a shotgun assembly are typically linked together in a graph structure that can serve to guide finishing and in some case close gaps in-silico. Also, in many cases, sequence composition of contigs can provide clues to fill gaps in scaffolds. A set of scripts to automate some of these tasks can be found here: Finishing Scripts v1.0 (63 MB tar.gz file).

http://www.cbcb.umd.edu/finishing/

Address of the bookmark: http://www.cbcb.umd.edu/finishing/

NGS Online Training

Sat, 27 Sep 2014 07:42:29 -0500

ArrayGen Technologies announces to provide online NGS training through out the globe. Now analyze your own NGS datasets from anywhere.For more information contact us at training@arraygen.com

Please visit our site at www.arraygen.com

PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool

Jit — Fri, 01 Dec 2017 04:10:54 -0600

PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms.

Relying on unique software architecture, PLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

PLAST stands for Parallel Local Sequence Alignment Search Tool and is was published in BMC Bioinformatics.

PLAST is a general purpose sequence comparison tool providing the following benefits:

PLAST is a high-performance sequence comparison tool designed to compare two sets of sequences (query vs. reference),
Reduces the processing time of sequences comparisons while providing highest quality results,
Contains a fully integrated data filtering engine capable of selecting relevant hits with user-defined criteria (E-Value, identity, coverage, alignment length, etc.),
Does not require any additional hardware, since it is a software solution. It is easy to install, cost-effective, takes full advantage of multi-core processors and uses a small RAM footprint,
Ready to be used on desktop computer, cluster, cloud as well as within distributed system running Hadoop.

https://plast.inria.fr/

Address of the bookmark: https://plast.inria.fr/

JRF in Bioinformatics @ INMAS, DRDO,Delhi

Wed, 01 Oct 2014 07:01:07 -0500

Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi under the aegis of Defence Research and Development Organisation (DRDO), is engaged in research and developmental work in radiation sciences, Neuro-Computing and Medical Image Processing. INMAS is looking for meritorious young researchers for pursuing research in the frontier areas at INMAS. The Institute invites applications from young and meritorious Indian nationals who are creative, have passion and desire to pursue R&D in frontier areas. INMAS possesses ambience of a research cum academic institute coupled with an advanced R&D infrastructure in a mission mode. It provides the best infrastructure, motivation and personality development prospects for talented students, dreaming of unparalleled success in their professional endeavors. INMAS provides state of the art research facilities for undertaking pioneering research with defence applications.

JRF (Maximum Tenure‐ Five Years: 2yrs as JRF and 3yrs as SRF)
A first class Master’s Degree in Bioinformatics (likely 2 posts)
Around Rs 16,000/ Plus 30% HRA (as per rules of funding agency)

Applications are invited from candidates possessing the above qualifications. The upper age limit is as on the last date for receipt of application. (5 years relaxation to SC/ST candidates, 3 years to OBC candidates, and other entitled categories as per Govt rules). Actual No. of vacancies may vary.

Application form can be download from the website www.drdo.gov.in and E Mailed to inmashrd@gmail.com.
Last date to apply by email is 1700 hrs on 15 Oct 2014
Incomplete applications are liable to be rejected.
Confirmation will be sent to short-listed candidates through email only
Antecedents of selected candidates will be verified.
Written Test will be conducted from 0930-1030 hrs. Latecomers will not be considered.
Candidates will be required to produce certificates/testimonials in original at the time of interview.
It may please be noted that offer of Fellowship does not confer on fellows any right for absorption in DRDO.
Candidates should carry photocopy of Application form sent by email with them.
No TA/DA will be paid for attending interview & on joining.
Last date to apply by email is 1700 hrs on 15 Oct 2014

More at http://drdo.gov.in/drdo/English/jrf29092014.pdf
http://drdo.gov.in/drdo/English/index.jsp?pg=inmas29092014.jsp

Porechop: tool for finding and removing adapters from Oxford Nanopore reads

Rahul Nayak — Tue, 29 May 2018 07:33:44 -0500

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

Address of the bookmark: https://github.com/rrwick/Porechop

Internship Program for Bioinformatics / Biotechnology Professionals (No. Of Vacancy: 2)

Wed, 08 Oct 2014 01:10:08 -0500

ArrayGen is offering an Internship Program for Post graduate Bioinformatics / Biotechnology students and professionals. ArrayGen Technologies provide an excellent opportunity to gain research experience and explore if a scientific career is right for you. Currently we offer positions to outstanding students interested in Next Generation Sequencing (NGS) data analysis. Applications are accepted throughout the year. Accepted students will be listed on web with their schedules. Accepted students can attend our future workshops and trainings freely at the specified venue.

Installing Salmon for Trinity !

Rahul Nayak — Tue, 03 Jul 2018 09:02:29 -0500

➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ conda install salmon
Solving environment: done

## Package Plan ##

environment location: /home/urbe/anaconda3

added / updated specs:
- salmon

The following packages will be downloaded:

package | build
---------------------------|-----------------
boost-1.64.0 | py36_4 331 KB conda-forge
jemalloc-5.1.0 | hfc679d8_0 8.2 MB conda-forge
boost-cpp-1.64.0 | 1 17.8 MB conda-forge
salmon-0.10.2 | 1 3.7 MB bioconda
conda-4.5.5 | py36_0 624 KB conda-forge
tbb-2018_20171205 | 0 1.2 MB conda-forge
------------------------------------------------------------
Total: 31.8 MB

The following NEW packages will be INSTALLED:

boost: 1.64.0-py36_4 conda-forge
boost-cpp: 1.64.0-1 conda-forge
jemalloc: 5.1.0-hfc679d8_0 conda-forge
salmon: 0.10.2-1 bioconda
tbb: 2018_20171205-0 conda-forge

The following packages will be UPDATED:

conda: 4.5.4-py36_0 conda-forge --> 4.5.5-py36_0 conda-forge

Proceed ([y]/n)? y

Downloading and Extracting Packages
boost-1.64.0 | 331 KB | ####################################################################################################################################### | 100%
jemalloc-5.1.0 | 8.2 MB | ####################################################################################################################################### | 100%
boost-cpp-1.64.0 | 17.8 MB | ####################################################################################################################################### | 100%
salmon-0.10.2 | 3.7 MB | ####################################################################################################################################### | 100%
conda-4.5.5 | 624 KB | ####################################################################################################################################### | 100%
tbb-2018_20171205 | 1.2 MB | ####################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

How far can bioinformatics go creating organisms used for testing?

Fri, 17 Oct 2014 02:08:16 -0500

"I think you can get very far on a technical level. The problem is that a human body is more complex than just one cell." ... "At some point we still need clinical tests on animals and humans before we use it for real treatment. But we will likely be able to remove 99 % of animal tests in the future." Erik Lindahl, Professor of Theoretical and Computational Biophysics at KTH Royal Institute of Technology is telling us about his work. From the episode "Science for life – mapping the building blocks of the human body". Watch the rest of the talk, and other talks at www.crosstalks.tv Crosstalks is an academic talkshow produced by KTH Royal Institute of Technology and Stockholm University.