<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/14800?offset=440 https://bioinformaticsonline.com/opportunity/view/8287/post-doc-in-computational-genetics-and-genomics-at-ceinge-biotecnologie-avanzate-naples-italy Tue, 11 Feb 2014 08:06:47 -0600 <![CDATA[Post doc in Computational Genetics and Genomics at CEINGE Biotecnologie Avanzate, Naples, Italy]]> We are seeking one motivated scientist to analyze genomics and transcriptomics data of a large collection of neuroblastoma tumors. The successful candidate will be part of a team of researchers with extensive expertise in genome cancer study. He/she will be involved in the analysis of DNA-seq, RNA-seq, ChIP-seq data using available methods running in R and UNIX environment.

Qualifications

PhD or Post-Graduated Master degree is required. Successful candidates will have some expertise in data analysis of NGS data by using methods running in R and UNIX environment. Familiarity with genome databases and browsers is required.

Application

Candidates should send a CV and a brief personal statement focusing on their skills and interests related to the research project.

Contacts

Start date: 1° April 2014
Salary on grant: 25,000 euros per year.
Contact Person (Referent): Mario Capasso
Ref. Email: mario.capasso@unina.it and achille.iolascon@unina.it
Tel: +39 081 3737889

]]> https://bioinformaticsonline.com/news/view/8317/new-version-of-modeller-913 Thu, 13 Feb 2014 09:07:57 -0600 https://bioinformaticsonline.com/news/view/8317/new-version-of-modeller-913 <![CDATA[New version of Modeller, 9.13]]> The new version of Modeller, 9.13, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information.

image

If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.13 - the same license key will work. (It won't do any harm to reregister if you want to, though!)

9.13 is primarily a bugfix release relative to the last public release(9.12). Major user-visible changes include:

# Modeller now includes a variety of SOAP (statistically optimized atomic potential) scores for assessing proteins, loops, and interfaces.

# The Lennard-Jones interaction energy is now artificially truncated at very short distance; this makes simulations with poor starting conditions much less likely to 'blow up'.

# model.get_insertions(), model.get_deletions() and model.loops() now have an include_termini option; if False, residue ranges that include chain termini are excluded from the output.

See the Modeller manual for a full change log: http://salilab.org/modeller/9.13/manual/node39.html

If you encounter bugs in Modeller 9.13, please see http://salilab.org/modeller/9.13/manual/node10.html for information on how to report them.

Reference:

http://salilab.org/modeller/

]]> Radha Agarkar https://bioinformaticsonline.com/opportunity/view/9055/computational-biologist-scientist-strand-life-sciences Fri, 14 Mar 2014 11:36:56 -0500 <![CDATA[Computational Biologist Scientist @ Strand Life Sciences]]> We are looking for a motivated application scientist to help evaluate, compare, and develop next generation sequencing (NGS) data analysis methods. The successful candidate should be able to quickly understand the state-of-art computational biology techniques, prototype them and perform benchmarking studies. The candidate must also be comfortable working with people from different disciplines and be able to present data analysis results in a clear and effective manner. The candidate is also expected to interact with customers as needed, write technical reports and publish new methods and/or data analysis findings in public forums.

Candidate Requirements: A PhD in computer science, computational biology, Bioinformatics, or a related field, along with sufficient programming skills for prototyping. Experience with next generation sequencing data analysis is required. Candidates with MS degree but with relevant work experience can also be considered. The successful candidate must be motivated and capable of working independently as well as in team environment.

Eligible and interested candidates can email your resumes to rohit at strandls dot com

About Strand Life Sciences: Strand was founded in 2000 by computer science and mathematics professors who recognized the need to automate and integrate life science data analysis through an algorithmic and computational approach. Strand’s solutions for life sciences research are robust and easy to use by the most novice user while powerful and configurable for the bioinformatician. Using its award-winning application development platform, AVADIS®, Strand builds innovative products that enable fast and cutting-edge analysis for basic and clinical research, drug discovery and development.

http://www.avadis-ngs.com/careers

]]> https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist Fri, 02 Mar 2018 06:54:15 -0600 https://bioinformaticsonline.com/pages/view/35805/python-learning-resources-for-bioinformatics-and-computational-biologist <![CDATA[Python learning resources for bioinformatics and computational biologist !]]> Python is a general-purpose language, which means it can be used to build just about anything, which will be made easy with the right tools/libraries.

Professionally, Python is great for backend web development, data analysis, artificial intelligence, and scientific computing. Many developers have also used Python to build productivity tools, games, and desktop apps, so there are plenty of resources to help you learn how to do those as well.

For pros and cons visit http://www.bestprogramminglanguagefor.me/why-learn-python and http://bioinformaticsonline.com/discussion/view/459/python-vs-perl

More resources at https://github.com/CodementorIO/Python-Learning-Resources

Following are the list of useful python programming resources:

]]> Jit https://bioinformaticsonline.com/researchlabs/view/8943/roth-lab Tue, 11 Mar 2014 17:43:45 -0500 <![CDATA[Roth Lab]]> The Roth Lab seeks insight into biological systems through genome- and proteome-scale experimentation and analysis.

Current computational interests:

Systematic analysis of genetic epistasis to identify redundant or compensatory systems and to reveal order of action in genetic pathways.
Using knockout, knockdown, or overexpression, or other perturbation experiments in combinations of genes in S. cerevisiae, C. elegans or mouse.
Using genome-scale genotyping of natural polymorphisms in S. cerevisiae and human populations.
Alternative splicing and its relationship to protein interaction networks.
Integrating large-scale studies including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns to quantitatively assign function to genes and guide experimentation.

More at http://llama.mshri.on.ca/index.html

]]> https://bioinformaticsonline.com/opportunity/view/9039/postdoc-position-in-computational-biology Fri, 14 Mar 2014 01:38:49 -0500 <![CDATA[Postdoc Position in Computational Biology]]> The Computational Biology Group of Interdisciplinary Center for
Clinical Research (IZKF) Aachen, RWTH Aachen University Hospital,
Aachen, invites applicants for PhD candidate or postdoctoral position
in computational biology in one of the following topics:

1) Statistical machine learning methods for the analysis of medical
epigenomics data.

2) Sequence analysis algorithms for detection of RNA-DNA interactions.

Applicants should hold a M.Sc . or PhD in Computer Science or related
areas. Experience in the analysis of biological sequences, gene
expression and gene regulation is desirable. The candidate should have
solid programming skills (C, Python and/or R) and acquaintance with
Linux. Experience with high performance computing is a plus. The
working language of the group is English.

The position is based on the German TV-L 13 salary scale, including
all German social benefits (health insurance and pension scheme). The
expected starting date is September 2014. Interested candidates should
send a CV, statement of research interests and the names of three
references to jobs@costalab.org.

More at http://costalab.org/wp/phd-and-postdoc-position-in-computational-biology/

]]> https://bioinformaticsonline.com/fun/view/9207/biogeek-fun Sun, 16 Mar 2014 06:33:31 -0500 https://bioinformaticsonline.com/fun/view/9207/biogeek-fun <![CDATA[BioGeek Fun]]> 1. A futuristic computational biology student was told to write "It is in my gene!!!" on the board 100 times as a punishment. here's his response -

use warnings;
for ($count=1; $count <=100; $count++) { print "It is in my gene!!!";}

I guess, he is gonna to be a real biogeek. Nice try though. Smart kid.

 

2. In some perl script I found this
 . . . . . .
 . . . . . .
# It works for me, only God understood how it is working
while (/(<\/[^>]+>)|(<[^>]+>)|(<[^>]+>)$|([^><]+)/go) {
            $startGene=$1;
            $beginChromosome=$2;
    
. . . . . .
 .. . . . . .
}

 

3. One more interesting message in Perl found …. It will must tickle you bone :)
open(my $fh, "<", "gene.txt")    or kill " Me if you think this is a mistake :$!";

 

4. From the Perl

  while () {  # "The Mothership Connection is here!"
    print “$_\n”; # Printing the offspring :)

 

5. Perl message
if ($1) { print “Just found a the error in chromosome !!!, yahoo…”; else { “That is not error, but mutation you moron!”;

 

6. One genome database curator walk in wine bar asked the bartender:
CREATE TABLE gene IF NOT EXISTS SexOnTheBeach;

]]> Jit https://bioinformaticsonline.com/news/view/39606/amity-university-bioinformatics-summer-program-kolkata Tue, 11 Jun 2019 21:27:10 -0500 https://bioinformaticsonline.com/news/view/39606/amity-university-bioinformatics-summer-program-kolkata <![CDATA[Amity University Bioinformatics Summer Program - Kolkata]]> Registrations are now open for the 2019 Summer Bioinformatics Training program at Amity University, Kolkata. The program will focus on introductory topics for life science students. We will review important history, topics and challenges bioinformatics can help address in the context of basic research, discovery and industry.

Read more: https://edu.t-bio.info/amity-university-summer-bioinformatics-program-registrations-are-open/

]]> eliabrodsky https://bioinformaticsonline.com/researchlabs/view/9327/jarvis%E2%80%99-laboratory Tue, 18 Mar 2014 18:53:47 -0500 <![CDATA[Jarvis’ laboratory]]> Dr. Jarvis’ laboratory studies the neurobiology of vocal communication. We want to know how the brain generates, perceives, and learns behavior. We use vocal communication as a model behavior. Emphasis is placed on the molecular pathways involved in the perception and production of learned vocalizations. We use an integrative approach that combines behavioral, anatomical, electrophysiological, and molecular biological techniques. The main animal model used is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations. The overall goal of the research is to advance knowledge of the neural mechanisms for vocal learning and basic mechanisms of brain function.

Lab page: http://jarvislab.net/

]]> https://bioinformaticsonline.com/opportunity/view/9518/professor-and-associate-professors-pb-iv-assistant-professors-pb-iii-job-at-iiit-allahabad Mon, 31 Mar 2014 08:09:07 -0500 <![CDATA[Professor and Associate Professors (PB-IV) Assistant Professors (PB-III) Job at IIIT, Allahabad]]> Indian Institute of Information Technology, Allahabad
Devghat, Jhalwa, Allahabad – 211012, Uttar Pradesh, India
E-mail: contact@iiita.ac.in, faculty.applications@iiita.ac.in
Web: www.iiita.ac.in Phone : 0532-2922031/27/67

Applications are invited on prescribed format along with self attested copies of the certificates for Faculty Positions in the following areas:
Sciences – Systems Biology, Computer Aided Drug Designing, Statistics, Applied Mathematics, Applied Physics. BioMedical Engineering – BioMechanics, BioMedical Instrumentation.

Last Date : May 10, 2014

Details are available on our website : http://www.iiita.ac.in

http://www.iiita.ac.in/downloads/announcements/uploads/FACULTY_Advertisement_NO-FS-01_2014130.pdf

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