CGHub
https://cghub.ucsc.edu/
Comprehensive data repository; huge data size

EGA
https://www.ebi.ac.uk/ega/
Comprehensive data repository; huge data size

COSMIC
http://cancer.sanger.ac.uk
Largest somatic mutation database; genome sequencing paper curation

CPRG
http://www.broadinstitute.org/software/cprg
Interface for cancer program resources

GDAC
http://gdac.broadinstitute.org/
Data analysis; automatic pipelines; user-friendly reports

SNP500Cancer
http://snp500cancer.nci.nih.gov
Sequence and genotype verification of SNPs

canEvolve
www.canevolve.org/
Comprehensive analysis of tumor profile; Data from 90 studies involving more than 10,000 patients

MethyCancer
http://methycancer.psych.ac.cn
Relationship among DNA methylation, gene expression and cancer

SomamiR
http://compbio.uthsc.edu/SomamiR/
Correlation between somatic mutation and microRNA; genome-wide displaying

cBioPortal
http://www.cbioportal.org/public-portal/
Graphical summaries; gene alteration; processed data; visualization

UCSC Cancer Genomics Browser
https://genome-cancer.soe.ucsc.edu/
Clinical information; gene expression; copy number variation; visualization

CGWB
https://cgwb.nci.nih.gov/
Visualization; gene mutation and variation; automated analysis pipeline

GDSC
http://www.cancerrxgene.org
Drug sensitivity information; drug response information

canSAR
https://cansar.icr.ac.uk/
Multidisciplinary information; drug discovery

NONCODE
http://www.noncode.org/ ncRNAs;
lncRNAs; up-to-date and comprehensive resource

Address of the bookmark: https://sourceforge.net/projects/genoviz/

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

The Cold Spring Harbor team's validation of Scalpel, published over the weekend in Nature Methods, compares Scalpel's performance on a live whole exome against HaplotypeCaller and SOAPindel. The donor is an individual with serious neurological disorders, which may be linked to a high incidence of indels. One thousand indels from this individual's exome, called by one or more of the informatics pipelines, were selected for focused resequencing. This resequencing revealed a 77% true positive rate for Scalpel calls, dramatically better than the rates for either of the competing tools; Scalpel performed especially well with indels longer than five base pairs, a traditional weak point for indel callers.

Finally, the authors demonstrate Scalpel's use on a large set of genetic data from nearly 600 families who donated samples to the Simons Simplex Collection, a project of the Simons Foundation Autism Research Initiative. Scalpel found a very high enrichment for indels in children affected by autism, compared with their unaffected siblings, a pattern that persisted even after excluding common variants.

Collaborative python library used in the DYOGEN teamfor studying the evolution of gene order in vertebrates.

http://www.ibens.ens.fr/?rubrique43&lang=fr

Address of the bookmark: https://github.com/DyogenIBENS/LibsDyogen

Algorithms scripts @ https://github.com/jschendel/bioinformatics-algorithms-coursera

Address of the bookmark: https://github.com/jorvis/biocode

Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes.

More at http://bioinf.spbau.ru/sibelia

Sibelia docs http://gensoft.pasteur.fr/docs/Sibelia/3.0.7/SIBELIA.md

Address of the bookmark: https://github.com/bioinf/Sibelia

WALK IN INTERVIEW

A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.

RA (One Post):

Salary : Rs. 11000 p.m. plus admissible HRA

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

Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” 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. No TA&DA will be given for attending the interview.

Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf

Project Scientist-I
Experimental / Computation analysis experience in highthroughput genomics/ clinical application.

Project Manager
Experience in handling large biological projects involving high-throughput genomics/ clinical application.

Scientific Administrative Assistant
Lab Work.

More at https://vinodscaria.genomes.in/positionsopen

Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.

i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.

ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).

iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.

iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.

v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.

Download application form from website: http://www.allduniv.ac.in/

Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014

For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf

Last Apply Date: 30 May 2014

LoVis4u is a bioinformatics tool for Loci Visualisation.

LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualising entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences.

https://art-egorov.github.io/lovis4u/

Address of the bookmark: https://github.com/art-egorov/lovis4u