BOL: Related items

RA Bioinformatics at Alagappa University

Sat, 08 Aug 2015 01:36:35 -0500

RA Bioinformatics

Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech)

Location : Chennai

Last Date : 20 Aug 2015

Hiring Process : Walk - In
Alagappa University - Job Details

RA Bioinformatics Job position in Alagappa University

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences

No.of Post: One

Salary : Rs. 11000
How to apply

A walk-in Interview will be held at the Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630 004 on 20.08.2015 (Thursday) at 10.30 AM.

Interested candidates are encouraged to send their Curriculum Vitae by email in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview.

Click Here for more http://alagappauniversity.ac.in/files/news_files/Notification.pdf

VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules

Rahul Nayak — Thu, 04 Oct 2018 16:30:44 -0500

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store only those read-pairs or reads who intersect some region around the variant locations. Alternatively, if your scientific question is focused on only one aspect of the data (e.g. breakpoints), many reads can be removed without losing the information relevant to the problem.

Address of the bookmark: https://github.com/broadinstitute/VariantBam

Bioinformatics Made Easy Search: Bioinformatics tools and run genomic analysis in the cloud

Rahul Nayak — Thu, 20 Aug 2015 02:21:20 -0500

InsideDNA makes hundreds of bioinformatics tools immediately available to run via an easy-to-use web interface and allows an accurate search across all functions, tools and pipelines.

With InsideDNA, you can upload and store your own genomic/genetic datasets in a limitless cloud space, and instantly analyze it with a powerful compute instance, without any tool installation or set up hassle.

More at https://insidedna.me/

Address of the bookmark: https://insidedna.me/

jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator

Abhimanyu Singh — Fri, 26 Jul 2019 00:58:12 -0500

jackalope simply and efficiently simulates (i) variants from reference genomes and (ii) reads from both Illumina and Pacific Biosciences (PacBio) platforms. It can either read reference genomes from FASTA files or simulate new ones. Genomic variants can be simulated using summary statistics, phylogenies, Variant Call Format (VCF) files, and coalescent simulations—the latter of which can include selection, recombination, and demographic fluctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as reads from Pacific Biosciences These simulations include sequencing errors, mapping qualities, multiplexing, and optical/PCR duplicates. All outputs can be written to standard file formats.

A swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope.lucasnell.com

Address of the bookmark: https://github.com/lucasnell/jackalope

JRF Position – International Institute of Information Technology, Hyderabad

Mon, 24 Aug 2015 22:44:46 -0500

International Institute of Information Technology, Hyderabad

Center for Computational Natural Sciences and Bioinformatics

Junior Research Fellowship Position

Applications are invited for one JRF position in the following DAE sponsored project.

Title of the project: Insight into the Structure–Function Relationships of Chemically Modified Nucleic Acids: A Molecular Dynamics Simulations Study.

The above project involves theoretical modelling and simulations on chemically modified nucleic acids to investigate their structures, dynamics and thermodynamic stabilities.

Desired qualification: M.Sc. in Chemistry/ Bioinformatics; GATE/UGC-CSIR NET qualification.

To apply: Send detailed curriculum vitae by e-mail to the following address on or before 31 August 2015: Prof. U. Deva Priyakumar (devalab@iiit.ac.in), CCNSB, IIIT-H, Gachibowli, Hyderabad 500 032.

genomics public data links !

Jit — Thu, 13 Feb 2020 00:20:00 -0600

List of publically available databases on google server.

More at https://software.broadinstitute.org/gatk/download/bundle

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

Cancer research database

Neel — Tue, 01 Sep 2015 17:36:31 -0500

Researchers in Andhra Pradesh have developed a database to identify genes that are common in tumours to provide their colleagues with easy access to insights into the genetic alterations in cancer.

The database, hosted at the Sri Venkateswara University (SVU) in Tirupati, will integrate information on cancer genes and markers with experimental data.

The Cancer Gene Markers Database (CGMD) is meant to help scientists better understand tumour genes and markers at a molecular level by combining data with literature on treatment regimen and recent advances in cancer therapy.

The database is free to access, and already includes 309 genes and 206 markers that correspond to 40 different human cancers. Accompanying literature comes from databases such as the United States’ National Center for Biotechnology Information and the Kyoto Encyclopedia of Genes and Genomes. It also includes experimental data from PubMed.

In a paper published last month in Nature Scientific Reports, the researchers from SVU’s department of animal biotechnology, describes the need for a database for different genes and markers along with their molecular characteristics and pathway associations.

Consed--A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Neel — Fri, 07 Feb 2020 07:16:22 -0600

Supports Illumina, 454, other Next-Gen and Sanger Reads and allows mixtures of these read types
Consed includes BamScape which can view bam files with unlimited numbers of reads. BamScape can bring up consed to edit reads and the reference sequence in targeted regions.
Consed is compatible with Newbler, Cross_match, Phrap, MIRA, Velvet and PCAP output.
Quickly takes the user to each variant site for viewing (also available as an automated report)
Overview of assembly can help detect and fix misassemblies
Editing time reduced by the program's ability to pin-point problem areas
Editing is guided by error probabilities

Address of the bookmark: http://www.phrap.org/consed/consed.html

Walk-in-interview for SRF, JRF posts at NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY New Delhi-110012

Thu, 10 Sep 2015 15:58:55 -0500

NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY New Delhi-110012

Eligible candidates may appear in Walk-in-interview for the positions of Senior Research Fellow in ICAR funded projects as follows

ICAR Network Project on Transgenics in Crops- Amelioration of cold induced sweetening in potato.

PI: Dr Debasis Pattanayak

SRF

Rs.25000/‐+ 30% HRA

September 29, 2015

Essential: Master’s Degree in Bioinformatics /Biotechnology/ Biochemistry/ life sciences with four years Bachelor’s Degree (or) Master’s Degree in Bioinformatics /Biotechnology/Biochemistry/ life sciences with NET qualification. .

Desirable: Experience in Bioinformatics and programming.

Age Limit: 35 years max. (5 years relaxation for SC/ST/OBC and woman candidates as per ICAR rules).

The post is purely temporary in nature and is co-terminus with the project. The interview will be held on September 29, 2015 at 10 AM at NRCPB, LBS Building, Pusa Campus, and New Delhi-110012. The candidates must bring four copies of biodata, original certificates, attested photocopies of each of the certificates and an attested copy of recent passport size photograph.

No TA/DA would be given for the appearance in interview. Only the candidates having essential qualifications would be entertained for the interviews

http://www.nrcpb.org/sites/default/files/NPTC%20walk%20in%20interview%20September%202015%20for%20NRCPB%20webpage%20D%20%20%20Pattanayak.pdf

Guest Faculty Job vacancies in Pondicherry University

Tue, 22 Sep 2015 23:50:16 -0500

Guest Faculty Job vacancies in Pondicherry University
Qualification : M.Phil. / M.Tech. / M.Sc. in Computer Science / Master of Computer Applications with a minimum of 55% of marks. Candidates with Ph.D. degree and NET/SLET qualification will be given preference as per UGC norms.

Desirable : Research or teaching experience in Bioinformatics and Computational Biology.
Honorarium : Rs. 1,000/- per lecture (subject to a maximum of 25,000/- per month)
How to apply

Interested eligible candidates may attend the 'walk-in' interview along with all original certificates and testimonials with a copy of their bio-data. Walk-in-interview will be held on 28.09.2015 (Monday), 03:00 P.M. at the office of the Dean, School of Life Sciences, Science Block — I, Pondicherry University, Puducherry — 605 014. Candidates reporting after 03:00 P.M. will not be entertained.

More at http://www.pondiuni.edu.in/news/walk-interview-guest-faculty-centre-bioinformatics