BOL: Related items

Walk in interview for Research Associate, Studentship and Traineeship at BIF, NEHU, Tura Campus

Thu, 18 Dec 2014 11:02:05 -0600

BIOINFORMATICS INFRASTRUCTURE FACILITY (BIF)
Department of RDAP
North-Eastern Hil University, Tura Campus
Tura-79402, Meghalaya

Walk in interview for Research Associate, Studentship and Traineeship at BIF

Applications are invited for the Post of Research Associate, Traineeship and Studentship in the DBT sponsored Bioinformatics Infrastructure Facility (BIF) at the Bioinformatics Centre, Department of RDAP, North-Eastern Hil University, Tura Campus, Tura-79402, Meghalaya. The Posts are purely temporary and terminable at any time without prior notice or assigning any reason thereof. The person engaged, shall not be entailed for any claim implicit or explicit for permanent absorption in the University.

Research Associate- 01

Essential Qualification: M.Sc. in Bioinformatics/Biotechnology from a recognized University/ institute.

Desirable: PhD or Pursuing PhD in the relevant subject(s) or equivalent published work in reputed peer reviewed journals or Advance PG diploma in Bioinformatics courses.

Duties: Creation of database, web designing, maintenance of internet, training of students in Bioinformatics, handling and knowledge of Bioinformatics software tools and technique, conducting Bioinformatics based research and other day to day laboratory work, writing report and scientific papers.

Pay:Rs. 2,00/- + Admissible 10% HRA per month

Age: Below 35 years

Traineeship- 02

Students who have completed Masters Degree in Bioinformatics/Biotechnology or any branch of Life Sciences/Agricultural Sciences/Computer Science to cary out a project work in Bioinformatics.

Desirable: Prior Knowledge of programming languages such as C, JAVA, MySQL is preferable.

Stipend: Rs. 800/- p.m. fixed. Purely temporary for a period of six months.

Studentship: 02

Students pursuing postgraduate degree in Bioinformatics/biotechnology/Agricultural Sciences or any branch of Life Science

Desirable: Prior knowledge of bioinformatics/ programming language is preferable.

Stipend: 800/- p.m. fixed. Purely temporary for a period of six months.

Candidates must send the detailed Biodata via mail/post and bring al the relevant documents in original and one set of attested photocopies of the same at the time of interview. No TA/DA will be paid for attending the interview and candidates have to make their own arrangements.

Last date for receiving application by mail or by post: 16.02.2014

Contact Information:
Dr.B.K. Mishra
Cordinator BIF,
RDAP Department, NEHU, Tura Campus
Phone: 91-03651-23107
Fax: 91-03651-23953
E-mail: drbkm1972@yaho.co.in, birendramishra14@gmail.com

Advertisement: http://www.nehu.ac.in/Advertisements/BIF_TuraAdtvPV_171214.pdf

BEDOPS v2.4.26: high-performance genomic feature operations

Jit — Mon, 12 Jun 2017 10:11:01 -0500

BEDOPS v2.4.26 is a suite of tools to address common questions raised in genomic studies — mostly with regard to overlap and proximity relationships between data sets. It aims to be scalable and flexible, facilitating the efficient and accurate analysis and management of large-scale genomic data.

The overview section of the BEDOPS v2.4.26 documentation summarizes the toolkit, functionality and performance enhancements. The reference table offers documentation for all applications and scripts.

Address of the bookmark: https://github.com/bedops/bedops

Assistant Professor at GAUHATI UNIVERSITY, GUWAHATI

Tue, 16 Dec 2014 01:15:30 -0600

Advt. No.T/2014/4

Ref. No. GU/Estt/T/308(VI)/2014/6451-61

Applications are invited from the Indian citizens for five (5) teaching posts of Assistant Professor (Contractual) under various departments of Gauhati University. Details of the advertisement, other terms and conditions and the application forms are available in the University website www.gauhati.ac.in

Asstt. Professor (Contractual)

2. M.Sc. Microbiology Course in Botany

3 1.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biochemistry (1 post). (Preference will be given to candidates having experience in Biochemistry).

2.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Bioinformatics).

3.M.Sc. Microbiology/M.Sc. Botany (Specialization in Microbiology)/M.Sc. Biotechnology(1 post). (Preference will be given to candidates having experience in Microbial Genetics).

As per UGC norms

Pay Band & Academic Grade Pay : (Consolidated pay) : Rs. 21,600/- per month

Application Form : Prescribe application form may download from the G.U. website www.gauhati.ac.in

Last date of receipt of filled-in application is 08.01.2015.

Advertisement: www.gauhati.ac.in/openfile.php?file=Notice1258.pdf

pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file

Jit — Thu, 24 May 2018 10:06:52 -0500

pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver option is specified.

Address of the bookmark: https://github.com/PacificBiosciences/pbalign

China University of Macau PhD Position 2015 in Bioinformatics, Computer Science

Mon, 22 Dec 2014 00:12:49 -0600

The Computational Biology and Bioinformatics Group at the University of Macau is inviting applications for PhD Position. Applicants will work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design. The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems. The duration of this PhD position is 2-3 years, starting in August 2015. Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month). The applications should be submitted before March 2015.

Study Subject(s): PhD position is award in the field of Bioinformatics/Computer Science.
Course Level: Position is available for pursuing PhD degree level at the University of Macau.
Scholarship Provider: University of Macau
Scholarship can be taken at: China

Eligibility: The ideal candidate would be a master degree holder in Bioinformatics or related disciplines with knowledge in Medical sciences or Life sciences (with GPA of at least 3.0 on a 4-point scale or equivalent) . Knowledge in programming (C and C++) and Linux scripting are necessary; experience in molecular docking, molecular dynamics simulations or molecular modeling is an advantage. The candidate should be fluent in spoken and written English; preference will be given to applicants with good publication records in relevant areas.

Scholarship Open for International Students: Researchers from China can apply for this PhD position.

Scholarship Description:

The Computational Biology and Bioinformatics Group at the University of Macau is looking for a motivated PhD student in Bioinformatics or Computer Science to work on a research project focusing on the flexible receptor protein-ligand docking algorithms for computer-aided drug design. The candidate will be working as part of a team in developing novel metaheuristic algorithms and scoring functions for large-scale, highly flexible protein-ligand docking problems.

Number of award(s): There is only one PhD position available.

Duration of award(s): The duration of this PhD position is 2-3 years.

What does it cover? Remuneration paid to candidate is MOP 11000-14000/month (~USD 1375-1750/month).

Selection Criteria: Not Known

Notification: Not Known

How to Apply: Send your current CV, your academic transcripts, a letter of motivation and research interests, two letters of recommendations from academic faculty to Dr. Shirley Siu at shirleysiu[at]umac.mo before March 2015.

Scholarship Application Deadline: The applications should be submitted before March 2015.

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

JNU Neuroscience/Systems Biology/Mathematical modeling JRF Vacancies

Fri, 26 Dec 2014 11:22:20 -0600

School of Computational and Integrative Sciences
Jawaharlal Nehru University
New Delhi 110067

Recruitment for Project

Applications were invited from the citizens of India for filling up the following temporary position for the CSIR sponsored Fellowship in the School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067. This position is temporary for a period of two and half years or tenable only for the duration of the project. The requisite qualifications & experience are given below.

Project Title : "Understanding Complex dynamics and Information processing in Brain Networks"
Funding Agency : CSIR

Principal Investigator : Dr. R.K. Brojen Singh

Position : Junior Research Fellow(One post)

Salary : As per CSIR rules and guidelines for JRF.

Qualifications & Experience : M.Sc. in Physics/Mathematics/Biology/B.Tech. In Eng. Physics/Comp. Sc. and desirable CSIR-UGC NET Qualified. Candidates should also have at least one years research experience after M. Sc./B.Tech. in works related to Neuroscience/Mathematical modeling.

Candidates possessing requisite qualifications may apply either on plain paper stating the project title along with CV and send to the following address or send as email attachment (pdf or word format) so as to reach on or before 8 January, 2014.

Dr. R.K. Brojen Singh
School of Computational and Integrative Sciences
Jawharlal Nehru University
New Delhi 110067
Email: brojen@jnu.ac.in, brojen@mail.jnu.ac.in

List of non-commercial NGS genotype-calling software

Jit — Thu, 09 Aug 2018 04:21:32 -0500

Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and quantify the considerable uncertainty associated with genotype calling, and will especially benefit the growing number of studies using low- to medium-coverage data.

A list of programs for genotype and SNP calling :

SOAP2 http://soap.genomics.org.cn/index.html

Single-sample High-quality variant database (for example, dbSNP) Package for NGS data analysis, which includes a single individual genotype caller (SOAPsnp)

realSFS http://128.32.118.212/thorfinn/realSFS/

Single-sample Aligned reads Software for SNP and genotype calling using single individuals and allele frequencies. Site frequency spectrum (SFS) estimation

Samtools http://samtools.sourceforge.net/

Multi-sample Aligned reads Package for manipulation of NGS alignments, which includes a computation of genotype likelihoods (samtools) and SNP and genotype calling (bcftools)

GATK http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit Multi-sample Aligned reads Package for aligned NGS data analysis, which includes a SNP and genotype caller (Unifed Genotyper), SNP filtering (Variant Filtration) and SNP quality recalibration (Variant Recalibrator)

Beagle http://faculty.washington.edu/browning/beagle/beagle.html

Multi-sample LD Candidate SNPs, genotype likelihoods Software for imputation, phasing and association that includes a mode for genotype calling

IMPUTE2 http://mathgen.stats.ox.ac.uk/impute/impute_v2.html

Multi-sample LD Candidate SNPs, genotype likelihoods Software for imputation and phasing, including a mode for genotype calling. Requires fine-scale linkage map

QCall ftp://ftp.sanger.ac.uk/pub/rd/QCALL

Multi-sample LD ‘Feasible’ genealogies at a dense set of loci, genotype likelihoods Software for SNP and genotype calling, including a method for generating candidate SNPs without LD information (NLDA) and a method for incorporating LD information (LDA). The ‘feasible’ genealogies can be generated using Margarita (http://www.sanger.ac.uk/resources/software/margarita)

MaCH http://genome.sph.umich.edu/wiki/Thunder

Multi-sample LD Genotype likelihoods Software for SNP and genotype calling, including a method (GPT_Freq) for generating candidate SNPs without LD information and a method (thunder_glf_freq) for incorporating LD information

Illumina Smartphone Chip !!!

Robert M Willioms — Tue, 30 Dec 2014 23:19:54 -0600

Illumina, the company that claims it brought human genome sequencing down to $1000 prices, has now turned its attention to a consumer product - a chip that you can plug into your smartphone and have it read your genetic information.

The biggest challenge ahead of Illumina is simplifying the process of genetic sequencing. Currently, Illumina’s DNA sequencers are gigantic machines that use techinques like colorimetry to work, but while the core technology is computational, it takes some 30 steps to extract genetic data and run it through. This process will likely have to be hugely simplified on mobile devices, given the fact that some studies require extracting 10 mililiters of blood. Illumina researchers are also working on finding the optimal technology for this on-chip DNA sequencing - be it electrical, optical, or other.

Illumina is one of the most prominent names in genetics, often said to be the Intel of genetic sequencing, as just like Intel it provides the algorithms, the processing brain that runs a DNA reading task.

In other recent smartphone-related biotech news, drug company Pfizer launched its REMOTE project, a new type of clinical trial that does not require going to a hospital for checks - targeted at patients with overactive bladder problems, the FDA-approved REMOTE project allowed to gather data from patients from over 10 states remotely, via mobile devices.

This is indeed the Illumina answer to Apple's Health app, HealthBook, Google HealthFit.

Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets

Neel — Sat, 06 Jul 2019 13:56:10 -0500

Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.

Developper: Gaëtan Benoit, PhD, former member of the Genscale team at Inria.

Contact: claire dot lemaitre at inria dot fr

Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets. https://gatb.inria.fr/software/simka/

Address of the bookmark: https://github.com/GATB/simka