BOL: Related items

RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities

Jit — Mon, 07 Aug 2017 18:49:27 -0500

RAMI, which clusters related nodes in a phylogenetic tree based on the patristic distance. RAMI also produces indices of cluster properties and other indices used in population and community studies on-the-fly.

Availability: RAMI is licensed under GNU GPL and can be run or downloaded from http://www.acgt.se/online.html.

Address of the bookmark: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp051

JRF Bioinformatics @ NATIONAL INSTITUTE OF IMMUNOLOGY NEW DELHI-110067

Fri, 17 Apr 2015 02:39:37 -0500

Applications are invited for the position of Junior Research Fellow (Project)/Senior Research Fellow (Project) for the following time-bound sponsored project as per the details given below:

1. “Development of bioinformatics methods for identifying novel secondary metabolites by genome mining” funded by DBT

JRF (P)/SRF (P) (One Position only)

Dr. Debasisa Mohanty Staff Scientist-VI deb@nii.res.in

Educational Qualifications: JRF (Project): M.Sc (Bioinformatics/ Biophysics/Biotechnology or any other stream of biological/physical sciences) or M.Tech. (Bioinformatics/Biotechnology/Computational Sciences) of M. Pharm.

SRF (Project): M.Sc (Bioinformatics/Biophysics/Biotechnology or any other stream of biological/physical sciences) or M.Tech. (Bioinformatics/Biotechnology/Computational Sciences) of M. Pharm with atleast 03 years of research experience.

Desirable Qualifications: Strong computer programming skills (in PERL/CGI/PHP or C++ or object oriented database management systems like MySQL etc or scripting languages under LINUX/UNIX environment) and sufficient experience in computational analysis of biological/biochemical data.

The candidates must highlight their experience in programming and database development in their CV. Job description: Computational analysis of genomes and development of bioinformatics tools and software’s for sequence and structure based analysis of biosynthetic pathways.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience JRF (Project): Rs. 12,000/- per month plus 30% HRA SRF (Project): Rs. 14,000/- per month plus 30% HRA (*Candidates possessing qualifications as per latest DST OM, will be given revised scales).

More at http://www1.nii.res.in/sites/default/files/projectappointments-Dr.DebasisaMohanty-30April2015.pdf

SMASH: An alignment-free tool to find and visualise rearrangements between pairs of DNA sequences

Jit — Thu, 21 Dec 2017 08:26:57 -0600

SMASH is a completely alignment-free method to find and visualise rearrangements between pairs of DNA sequences. The detection is based on relative compression, namely using a FCM, also known as Markov model, of high context order (typically 20). The method has been approached with a tool (also called SMASH). For visualization, SMASH outputs a SVG image, with an ideogram output architecture, where the patterns are represented with several HSV values (only value varies). The following image, illustrating the information maps between human and chimpanzee for the several chromosomes, depicts an example:

Address of the bookmark: https://github.com/pratas/smash

IGIB Recruitment 2015 – Project Scientist

Tue, 14 Apr 2015 12:19:59 -0500

IGIB Recruitment 2015 – Project Scientist & SPF Posts: CSIR – Institute of Genomics & Integrative Biology (IGIB) has issued notification for the recruitment of Project Scientist, Sr Project Fellow vacancies on temporary basis for project entitled “Setting up of CSIR(unit)-TRISUTRA (Translational research and Innovative Science through Ayurgenomics)”. Eligible candidates may apply in prescribed application format on or before 23-04-2015. Other details like age limit, educational qualification, selection process & how to apply are given below…

IGIB Vacancy Details:
Total No. of Posts: 04
Name of the Posts:
1. Project Scientist (Biology): 02 Posts
2. Project Scientist (Bioinformatics): 01 Post
3. Sr Project Fellow (Ayurveda): 01 Post

Age Limit: Candidates age should be 35 years for post 1, 32 years for post 2

Educational Qualification: Candidates should have Ph.D/ Ph.D submitted in any branch of Biological Science/ Life Science for post 1, Ph.D/ Ph.D submitted in Bioinformatics for post 2, BAMS degree with one year internship for post 3.

Selection Process: Candidates will be selected based on their performance in interview.

How to Apply: Eligible candidates may send their application along with all relevant documents on or before 23-04-2015.

Important Dates:
Last Date for Receipt of Application for Post 1 & 2: 23-04-2015.
Date of Interview for Post 3: 27-04-2015.

For other details like pay scale, age relaxation, educational qualification, selection process, how to apply, etc., click on the link given below…

http://www.freejobalert.com/wp-content/uploads/2015/03/Notification-IGIB-Project-Scientist-SPF-Posts.pdf

http://www.igib.res.in/sites/default/files/27042015.pdf

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

Jit — Thu, 19 Apr 2018 08:06:03 -0500

Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html).

Address of the bookmark: https://github.com/meiji-bioinf/heap

BINC Sample Question Paper !!!

Jitendra Narayan — Thu, 16 Apr 2015 09:14:14 -0500

BINC sample question paper round TWO.

BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data

Jit — Thu, 31 May 2018 09:35:23 -0500

BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a variant of the classical spectrum alignment algorithm introduced by Pevzner et al (2001). It uses an exhaustive search to find a k-mer path through a read that minimizes a heuristic objective function jointly considering penalties on correction, quality and k-mer support. This algorithm was first implemented in my fermi assembler and then refined a few times in fermi, fermi2 and now in BFC. In the k-mer counting phase, BFC uses a blocked bloom filter to filter out most singleton k-mers and keeps the rest in a hash table (Melsted and Pritchard, 2011). The use of bloom filter is how BFC is named, though other correctors such as Lighter and Bless actually rely more on bloom filter than BFC. https://github.com/lh3/bfc

Address of the bookmark: https://github.com/lh3/bfc

Bioinformatics JRF/RA/SRF position at Indian Institute of Science Education and Research (IISER Kolkata) - Kolkata, West Bengal

Fri, 17 Apr 2015 04:11:14 -0500

Research Position in Computational Biology in the group of Shree P. Pandey Positions available in the area of NGS data analysis, bioinformatics, plant genomics

Project Description: Projects involves high throughput analysis of data mostly generated by massively parallel sequencing (RNA-Seq and small-RNA-Seq), microarrays and related platforms. We are looking for highly motivated and bright individuals interested in high-throughput cutting-edge data analyses methods in genomics (computational positions). Available positions: Applications are invited from suitable candidates in both, the Max Planck India Partner Program and the CRP Wheat Program for openings at the levels:

Post Name-Qualification-Salary:
Project assistant – Master’s – Rs. 14000
Project fellow (junior data analyst) – Masters + research experience – Rs. 16000
Research fellow (senior data analyst) – Masters + adequate research experience/desirable skill sets – Rs. 22000
Research Associated – PhD (< 1yr) /> 1 yr experience – Rs. 28000 / Rs. 32000
Essential qualification: MSc/MTech/PhD (or other suitable qualification) in discipline related to bioinformatics, computational biology, computer application (or equivalent)/ ‘Advance Post-Graduate Diploma in Bioinformatics’. Proficiency in one of the programming languages or statistics (proficient in R for example) is compulsory.
Desirable qualification: 1. Programming experiences in at least one low level language such as C/C++ and one scripting language such as Perl/Python/PHP and knowledge of SQL/MySQL. 2. Substantial experience in the linux or other unix environments. 3. Experience of working in projects on Bioinformatics, Genetics or Biological application areas/Computational and Statistical analysis (e.g. using R or Matlab). Experience in the field of genomics (NGS, microarrays, genome annotation), database development and management, software development, systems and network biology (or related fields) will be preferred.
SELECTION PROCEDURE FOR INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH (IISER KOLKATA) – RESEARCH ASSOCIATE & MORE VACANCIES POST:

Candidates can apply on or before 30/04/2015
No Detailed information about the selection process is mentioned in the recruitment notification
HOW TO APPLY FOR RESEARCH ASSOCIATE & MORE VACANCIES IN INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH (IISER KOLKATA):

Applications should contain CV along with brief description (maximum 1 page) of research conducted (highlighting skills and experience) till now. Applications should be sent by email to Shree P. Pandey, Department of Biological Sciences, IISER-Kolkata, Mohanpur Campus, West Bengal within 2 weeks. Interviews will be scheduled within 10 days of closing of applications. E-mail: sppiiserkol@gmail.com, sppandey@iiserkol.ac.in
For more details visit: http://www.iiserkol.ac.in/~sppandey

Epiviz: an interactive visualization tool for functional genomics data.

Jit — Mon, 09 Jul 2018 05:27:39 -0500

Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. It also includes data from the Gene Expression Barcode project for transcriptome visualization. It has a flexible plugin framework so users can addd3 visualizations. You can see a video tour here.

https://bioconductor.org/packages/release/bioc/html/epivizr.html

https://github.com/epiviz

https://github.com/epiviz/epiviz

Address of the bookmark: https://epiviz.github.io/

Project Fellow Bioinformatics at Central Drug Research Institute

Mon, 27 Apr 2015 20:15:45 -0500

Project Fellow (Bioinformatics)
Central Drug Research Institute
Address: Chattar Manzil, M.G.Road, Kaisarbagh
Postal Code: 226001
City: Lucknow
State: Uttar Pradesh
Pay Scale: Rs.16,000/- (fixed) p.m.
Educational Requirements: M.Sc. in Bioinformatics with 55% marks for Gen. & OBC and 50% marks for SC/ST candidates, Physically and Visually handicapped candidates
Experience Requirements: Experience in computer-assisted scientific research in the area of Drug Design including Bio- molecular modeling and simulation studies, Virtual screening, pharmacophore perception, QSAR etc. Familiarity with Linux/Unixbased computer systems and required to participate and contribute to the development and application of computational models for the design and discovery of novel molecules as inhibitors or chemical probes
Details will be available at: http://cdriindia.org/uploaded/advt_no01-2015.pdf

How To Apply: Eligible candidates required to report for the Interview at 9:00 A.M. sharp on 11-05-2015 (For Position Code No. 001 to 009) and 12-05-2015 (For Position Code No. 010 to 016). Candidates reporting after 10:00 A.M will not be allowed to attend the interview. Eligible candidates may appear before the Selection Committee for interview on the date and time mentioned above at CDRI, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow-226031. Eligible candidates must bring with them duly filled up application form (which can be downloaded from our website www.cdriindia.org), along with Original certificates as well as attested copies of certificates of examinations starting from matriculation, date of birth, caste certificate (in case of SC/ST/OBC) experience certificate, publication, if any and recent passport size photograph etc. Original documents are essential for verification of the particulars quoted by the candidate in the application form and candidate failed to produce original documents at the time of verification, shall not be allowed to attend the interview. Any request for relaxation in this regard shall not be entertained.
Detail of Interview: 11-05-2015
Age Limit: 28 Years