BOL: Related items

CIAB Recruits Scientist, Engineer, Informatics Officer

Sat, 28 Nov 2015 03:40:28 -0600

Center of Innovative and Applied Bioprocessing (CIAB) - Punjab

Center of Innovative and Applied Bioprocessing (CIAB) invites applications to recruit on vacant posts of Scientist, Associate Plant Manager/ Plant Engineer, Informatics Officer. Applications against these Government Jobs can be submitted on or before 7th January 2016.
CIAB Vacancy 2015 Details

9. Research & Development – Informatics Officer
Qualification: M. Tech or M.E. in computer science or information technology or bioinformatics with 4 years of R&D experience (after Master’s Degree) in an R&D organization with work profile of large data assembly, analysis.
Age Limit: 45 years
How to Apply : Duly filled-in applications in prescribed application format along with copies of required documents should be reach to: Chief Exec

ASSISTANT PROFESSOR Bioinformatics at ALAGAPPA UNIVERSITY

Thu, 03 Dec 2015 23:30:43 -0600

ALAGAPPA UNIVERSITY
Recruitment and Sarkari Naukri for the Post of ASSISTANT PROFESSOR Bioinformatics
Job Description UGC scale of pay is applicable. For eligibility qualifications and other norms, please refer to the ?Instructions to the Candidates? available with the application forms which can be had on payment of Rs.520/- inclusive of Rs.20/- for postage. For SC/ST, Rs.320/- inclusive of Rs.20/- for postage on enclosure of a copy of the community certificate. Payment is to be made by means of Demand Draft drawn on any nationalized bank in favour of ?The Registrar, Alagappa University? payable at Karaikudi. Candidates can also download the application form and instructions to the candidates from httpwww.alagappauniversity.ac Filled-in application should reach on or before 19.10.2015
Salary for Job : Rs.15600-39100+AGP Rs.6000
Education : Good academic record with at least 55 marks (or an equivalent grade in a point scale wherever grading system is followed) at the Masters Degree level in a relevant subject from an Indian University, or an equivalent degree from an accredited foreign university. Besides fulfilling the above qualifications, the candidate must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/SET.Notwithstanding anything contained in sub-clauses (i) and (ii) above, the candidates, who are, or have been awarded a Ph.D. degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulations 2009, shall be exempted from the requirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor or equivalent positions in Universities/Colleges/Institutions.
Number of Vacancies : 02
Naukri Location : Other City(s) in Tamil Nadu
Address : KARAIKUDI ? 630 003
Last Date to Apply : 2015-12-04
Apply Process : written test/interview

MAKER

Jitendra Narayan — Sun, 07 Feb 2016 15:59:24 -0600

MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

More at http://www.yandell-lab.org/software/maker.html

Address of the bookmark: http://www.yandell-lab.org/software/maker.html

liftover

Jitendra Narayan — Mon, 08 Feb 2016 15:45:03 -0600

Convenient conversions between genome assemblie. The liftover package makes it easy to remap genomic coordinates to a different genome assembly.

More at https://github.com/aaronwolen/liftover

https://www.bioconductor.org/help/workflows/liftOver/

Address of the bookmark: https://github.com/aaronwolen/liftover

Stacks

Jitendra Narayan — Wed, 24 Feb 2016 15:52:30 -0600

Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

More at http://catchenlab.life.illinois.edu/stacks/

Address of the bookmark: http://catchenlab.life.illinois.edu/stacks/

scikit-learn

Jitendra Prajapati — Mon, 29 Feb 2016 17:39:24 -0600

Machine Learning in Python

Simple and efficient tools for data mining and data analysis
Accessible to everybody, and reusable in various contexts
Built on NumPy, SciPy, and matplotlib
Open source, commercially usable - BSD license

More at http://scikit-learn.org/stable/index.html

Address of the bookmark: http://scikit-learn.org/stable/auto_examples/index.html

MEDEA: Comparative Genomic Visualization with Adobe Flash

Jit — Tue, 26 Apr 2016 12:15:16 -0500

As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets.

More at http://www.broadinstitute.org/annotation/medea/

Address of the bookmark: http://www.broadinstitute.org/annotation/medea/

Ribbon !!

Jit — Fri, 21 Oct 2016 04:54:30 -0500

Visualization has played an extremely important role in the current genomic revolution to inspect and understand variants, expression patterns, evolutionary changes, and a number of other relationships. However, most of the information in read-to-reference or genome-genome alignments is lost for structural variations in the one-dimensional views of most genome browsers showing only reference coordinates. Instead, structural variations captured by long reads or assembled contigs often need more context to understand, including alignments and other genomic information from multiple chromosomes. We have addressed this problem by creating Ribbon (genomeribbon.com) an interactive online visualization tool that displays alignments along both reference and query sequences, along with any associated variant calls in the sample. This way Ribbon shows patterns in alignments of many reads across multiple chromosomes, while allowing detailed inspection of individual reads (Supplementary Note 1). For example, here we show a gene fusion in the SK-BR-3 breast cancer cell line linking the genes CYTH1 and EIF3H. While it has been found in the transcriptome previously, genome sequencing did not identify a direct chromosomal fusion between these two genes. After SMRT sequencing, Ribbon shows that there are indeed long reads that span from one gene to the other, going through not one but two variants, for the first time showing the genomic link between these two genes (Figure 1a). More gene fusions of this cancer cell line are investigated in Supplementary Note 2. Figure 1b shows another complex event in this sample made simple in Ribbon: the translocation of a 4.4 kb sequence deleted from chr19 and inserted into chr16 (Figure 1b). Thus, Ribbon enables understanding of complex variants, and it may also help in the detection of sequencing and sample preparation issues, testing of aligners and variant-callers, and rapid curation of structural variant candidates (Supplementary Note 3). In addition to SAM and BAM files with long, short, or paired-end reads, Ribbon can also load coordinate files from whole genome aligners such as MUMmer. Therefore, Ribbon can be used to test assembly algorithms or inspect the similarity between species. Supplementary Note 4 shows a comparison of gorilla and human genomes using Ribbon, highlighting major structural differences. In conclusion, Ribbon is a powerful interactive web tool for viewing complex genomic alignments.

Script at https://github.com/MariaNattestad/ribbon

Address of the bookmark: http://genomeribbon.com/

IMPUTE2

Jit — Thu, 27 Oct 2016 11:21:44 -0500

IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes. Most people use just a couple of the program's basic functions, but we have also built up a collection of specialized and powerful options. If you are new to IMPUTE2, or indeed to phasing and imputation in general, we suggest that you start by learning the basics.

You should begin by downloading the program from here. You will need to choose the link that matches your computing platform and then follow the instructions for opening the download package.

Once you have done this, you will be ready to try some example analyses on the test data that are provided with the download. The section on Examples shows how to use the most common IMPUTE2 functions. We suggest that you work through these examples and try to understand what the elements of each command are doing. If you don't understand something or would like to know if the program can perform a function that isn't listed, you can read our FAQ or submit a question to our mail list.

When you have learned the basic functionality of the program, you can use several features of this website to prepare your own analysis:

Learn about best practices for imputation.
Download reference data that you can use to impute genotypes in your study.
Look through a complete list of program options.

Address of the bookmark: https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

Research Associate and Junior Research Fellow at North-Eastern Hill University - Tura, Meghalaya

Fri, 28 Oct 2016 09:54:43 -0500

Research Associate and Junior Research Fellow
North-Eastern Hill University - Tura, Meghalaya
₹18,000 a month
Applications are invited for the post of Research Associate and JRF in the DBT sponsored Bioinformatics Infrastructure Facility (BIF), posts are purely temporary and terminable at anytime without prior notice or assigning any reason thereof.

Research Associate :
Essential Qualification: Ph.D in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.36000-/- + Admissible 10% HRA per month
Age: Below 35 years

Junior Research Fellow
Essential Qualification: M.Sc in Bioinformatics/Biotechnology/Life Science from a reocngised univeristy/institute
Pay: Rs.18000-/- + per month
Age: Below 35 years

Last date for receving application by mail or post is 08.11.2016

Company Info.
North-Eastern Hill University

Bioinformatics Infrastructure Facility (BIF) Department of RDAP North-Eastern Hill University, Tura Campus Tura-794002, Meghalaya

More at http://www.nehu.ac.in/Advertisements/BIFTuraManpowerAdvt_25102016.pdf