<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/31087?offset=370 https://bioinformaticsonline.com/news/view/19090/deeptools Sat, 08 Nov 2014 15:02:08 -0600 https://bioinformaticsonline.com/news/view/19090/deeptools <![CDATA[deepTools]]> deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats. By doing so, deepTools allows the creation of normalized coverage files or the comparison between two files (for example, treatment and control). Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome.

Publicaton: http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365.full

Source Code and Wiki: https://github.com/fidelram/deepTools/wiki

Galaxy Tool Shed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

and example Galaxy workflows: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows

]]> Martin Jones https://bioinformaticsonline.com/bookmarks/view/19631/rosalind-bioinformatics-problems Thu, 18 Dec 2014 10:32:48 -0600 https://bioinformaticsonline.com/bookmarks/view/19631/rosalind-bioinformatics-problems <![CDATA[Rosalind Bioinformatics problems !!!]]> Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

http://rosalind.info/problems/list-view/

Address of the bookmark: http://rosalind.info/problems/list-view/

]]> Abhi https://bioinformaticsonline.com/view/19838 Sat, 27 Dec 2014 13:30:15 -0600 https://bioinformaticsonline.com/view/19838 <![CDATA[Interview with a bioinformatician series ...]]> The aim of this series to interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.

This series will be available at BOL every fortnight.



]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/26993/lastz Mon, 18 Apr 2016 04:41:55 -0500 https://bioinformaticsonline.com/bookmarks/view/26993/lastz <![CDATA[LASTZ]]> LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

More at http://www.bx.psu.edu/~rsharris/lastz/

Thesis: http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf

Address of the bookmark: http://www.bx.psu.edu/~rsharris/lastz/

]]> Abhi https://bioinformaticsonline.com/videolist/watch/2791/ncbi-psi-blast-tutorial Fri, 23 Aug 2013 02:25:02 -0500 https://bioinformaticsonline.com/videolist/watch/2791/ncbi-psi-blast-tutorial <![CDATA[NCBI PSI-BLAST Tutorial]]> http:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are related to a sequence that the user provides.]]> https://bioinformaticsonline.com/fun/view/23959/bioinformatics-jokes Fri, 21 Aug 2015 01:26:54 -0500 https://bioinformaticsonline.com/fun/view/23959/bioinformatics-jokes <![CDATA[Bioinformatics Jokes !!]]> Why was the Bioinformatics fired from his job?

A: He was getting too Sassy.

 

What did the bioinformatician say when he found out his team stopped using version control?

A: Y’all better Git!

 

Why did the computational biologist stay home from work?

A: He had a code!

 

Why was the bioinformatician's paper was rejected?

A: Journal thought it seemed scripted.

 

How can you tell that a Bioinformatics is working?

A: You can hear him Grunting!

 

Why bioinformatician always silence?

A: Because bioinformatician calmly whisper, “SSH”

 

Why was the bioinformatician always so sleepy?

A: He/She wasn’t given any Java.

 

Why did the program/software hanged?

A: Because genome float.

 

Why was the class upset that its parent died?

A: Because it wouldn’t be getting the inheritance!

 

Why did bioinformatician always works on the command line?

A: Because they don't want to scare you with huge amount of data!

 

Why did the bioinformatician attend the gay pride parade?

A: They supported polymorphism.

 

Why did bioinformatician prefer awk, PerlOneliner?

A: Because even computer can't handle to load the data.

 

Why don’t bioinformatician get along with others?

A: They’re too MEAN.

 

Why computational biologist are cool?

A: Because they are scripted!!

 

Why they talk $ unzip; strip; touch; finger; grep; mount; fsck; more; yes; fsck; fsck; umount; clean; sleep;

A: Ah, Ohhh, dude, these are *NIX commands

 

Did they really hack genome?

A: Yes, I guess so.

]]> Jitendra Prajapati https://bioinformaticsonline.com/opportunity/view/24178/essentials-of-statistics-and-data-analysis-using-r Mon, 31 Aug 2015 01:32:12 -0500 <![CDATA[Essentials of Statistics and Data Analysis using R]]> Clinical Development Services Agency (CDSA) is an extramural unit of Translational Health Science and Technology Institute (THSTI), Department of Biotechnology, Ministry of Science & Technology, Government of India. CDSA has a national mandate of strengthening capacity and capability building in the area of Clinical development and Translational Research.

CDSA is pleased to announce a 4 days hands-on training program on “Essentials of Statistics and Data Analysis using R” at ICGEB, Aruna Asaf Ali Road, New Delhi on December 1 – 4, 2015. This will involve developing and enhancing skills to understand basic principles of statistics for summarizing data and use of appropriate statistical tests as well as providing an understanding of data analysis using R. Didactic lectures with practical sessions will be delivered by experienced faculties from AIIMS and Novartis. Live classroom with power point presentations, case studies, mock exercise, practical sessions on R, group work with time for discussion and Q&A sessions are added advantages of this workshop.

Please contact gayatrivishwakarma.cdsa@thsti.res.in or vineetabaloni.cdsa@thsti.res.in for program and registration details.

Please nominate personage or register yourself on or before November 6, 2015 along with the electronic transfer of registration fee.

]]> https://bioinformaticsonline.com/opportunity/view/24298/staff-scientists-at-national-institute-of-plant-genome-research-new-delhi Fri, 04 Sep 2015 22:06:59 -0500 <![CDATA[Staff Scientists at National Institute of Plant Genome Research, New Delhi]]> National Institute of Plant Genome Research, New Delhi is an Autonomous Research Institution funded by Department of Biotechnology, Ministry of Science & Technology, Govt. of India, to pursue research on various aspects of plant genomics. The Institute is also in the process of establishing a NIPGR Translational Centre at Biotech Science Cluster, NCR, Faridabad. NIPGR invites applications from Indian Citizens for filling up the vacant posts on Direct Recruitment basis, as detailed below. The posts are temporary but likely to continue.

Staff Scientists

Specialization: Applicant should have a Ph.D. with excellent academic credentials along with the track record of scientific productivity evidenced by publications/patents/products in the frontier areas of Plant Biology such as, Computational Biology, Genome Analysis and Molecular Mapping, Molecular Mechanism of Abiotic Stress Responses, Nutritional Genomics, Plant Development and Architecture, Plant Immunity, Molecular Breeding, Transgenics for crop improvement and other emerging areas based on plant genomics.

Remuneration: The length of experience and scientific accomplishments/quality of scientific productivity record will be major factors in deciding the level of appointment as Staff Scientist as well as starting salary in the Pay Bands of Rs 15,600-39,100 (with grade pay of 5400), and Rs 37,400-67,000 (with grade pay of 8,700 and 8,900) plus usual allowances admissible to the Central Government employees. However, NIPGR reserves the right to select candidates in the lower grade against the foregoing posts depending upon the qualifications and experience of the candidate. Reservation of posts shall be as per Govt. of India norms. Five posts (SC-2, ST-1, OBC-2) in the Pay Band of Rs 15,600-39,100 with Grade Pay of Rs 5400, are reserved.

More at http://www.nipgr.res.in/careers/vacancies_latest.php#

Apply online at http://www.nipgr.res.in/nipgr_recu/nipgr_recu.php

Form http://www.nipgr.res.in/files/careers/Application_Performa_2015.doc

]]> https://bioinformaticsonline.com/opportunity/view/24463/project-fellow-at-indian-institute-of-chemical-biology-iicb Tue, 22 Sep 2015 23:47:35 -0500 <![CDATA[Project Fellow at Indian Institute of Chemical Biology (IICB)]]> Advertisement No. : R&C/CD/427/2015 ,Vacancy Code: 4271501

Project Fellow Bioinformatics recruitment in Indian Institute of Chemical Biology (IICB) purely temporary

Name of the Project: "Genomics and Informatics Solutions for Integrating Biology(Genesis)".

No. of Vacancies: 1

Qualification required : M.Sc in Bioinformatics with 55% Marks.

Experience (Desirable): Candidate should be well versed with sequencing data analysis,assembly and annotation of whole genome sequence. Experience in transcriptional data analysis is also preferred.

Age Limit : 28 Years

Stipend : Rs.16000
How to apply
Interested candidates may appear for the walk-in-interview to be held on 28.09.2015 from 11.00 a.m. in the Red Carpet Room with the following documents self attested copy - (1) Matriculation Certificate in support of your date of birth, (2) Degree/Diploma Certificate, (3) Original reprints of all testimonials regarding educational qualification, (4) No Objection Certificate from the employer if employed, (5) Final Mark Sheet of M.Sc. Examination, (6) One Passport size photograph.

http://www.career.iicb.res.in/Recruitment%20Notice.php

]]> https://bioinformaticsonline.com/opportunity/view/24704/2-positions-on-the-evolutionary-analysis-of-biological-sequences-in-montpellier-france Mon, 28 Sep 2015 08:25:48 -0500 <![CDATA[2 positions on the evolutionary analysis of biological sequences in Montpellier - France]]> The Methods and Algorithms for Bioinformatics (MAB) team at the LIRMM (computer science, robotics and microelectronics laboratory at the CNRS & University of Montpellier, France) is looking for talented individuals to fill two postdoctoral positions. We are seeking candidates with a strong background in computational evolutionary biology. The positions will start by the end of 2015.

The first of the positions (duration: 18-24 months), associated with the European VIROGENESIS project (http://www.kuleuven.be/english/research/EU/p/horizon2020/sc/sc1/Virogenesis), concerns the evolutionary analysis of viral sequences. Topics include -- but are not limited to -- phylogenetic classification of metagenomic reads and the recombination history of viruses.

The second position (duration: 1 year), associated with the Institute for Computational Biology (IBC, http://www.ibc-montpellier.fr), concerns evolutionary analyses of large-scale genomic data -- including the inference of very large phylogenies, gene/species tree reconciliation, comparative genomics, phylogenetic network inference and verification, phylogeography, the use of phylogenies to study the evolution of characters.

A one thousand year old city, Montpellier is a thriving research community with a multitude of biology and biomedical research centers. It is the fastest growing city in France where approximately one third of the population are students, and a wonderful location for outdoor activities (kite/wind surfing, sailing, river/sea kayaking, hiking and rock climbing). The LIRMM is one of the most visible computer science laboratories in France.

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