BOL: Related items

The 2014 CeMM PhD Program

Wed, 05 Feb 2014 06:03:15 -0600

For our next PhD Program starting in October 2014 we are looking for exceptionally motivated PhD candidates with a keen interest in genomics and medicine and a strong interest to work in teams.

The 2014 CeMM PhD Program will focus on two thematic areas: INFECTION and CANCER, that are built on the pillars of epigenetics, bioinformatics and systems biology, chemical biology and the mechanism of action of drugs, high-throughput genetics, genomics and proteomics, and molecular and cell biology.

The choice of this strategic focus rests on the synergies between immunology, infection and cancer in pathophysiological and technological terms. It furthermore reflects the strength of the current CeMM faculty, itself built around the historical and contemporary expertise in immunology and cancer of the Medical University of Vienna.

As a CeMM PhD student you will get the chance to work at the cutting edge of interdisciplinary molecular medicine research and be trained by the entire CeMM and associated faculty to become one of the scientists shaping the future of molecular medicine.
Requirements

To be eligible to enroll in the CeMM PhD Program all candidates are required to have a bachelor’s or master’s degree in medicine, biology, chemistry, bioinformatics, mathematics or any scientific/technical, subject-relevant degree. Candidates do not need to have completed their degree at the time of application, however they must have obtained their final degree certificate by mid-September. The working language at CeMM is English, so excellent written and oral communication skills in English are required.
Timeline

Applications open on 20th January and close on 20th March 2014.
Two references are required to be submitted through the online system by 31st March 2014.
All complete candidate applications are reviewed by the CeMM Faculty in early April.
Selected candidates are invited to a Skype panel interview in late April.
Shortlisted candidates are then invited to Vienna in May for a full interview process, including an opportunity to introduce yourself through a presentation and interview rounds, meet research group members, and attend an informal dinner to get to know the Faculty members and learn more about their research.
Positions are offered by CeMM Faculty in June.
Start of PhD Program: 1st October 2014 .

Contact

Binia Maria Günther, BEd BA
Human Resources Manager
bguenther@cemm.oeaw.ac.at

Catherine Lloyd, Ph.D.
PhD and Postdoc Program Manager
clloyd@cemm.oeaw.ac.at

More Info: www.cemm.oeaw.ac.at/phd-program/application/

Installing Salmon for Trinity !

Rahul Nayak — Tue, 03 Jul 2018 09:02:29 -0500

➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ conda install salmon
Solving environment: done

## Package Plan ##

environment location: /home/urbe/anaconda3

added / updated specs:
- salmon

The following packages will be downloaded:

package | build
---------------------------|-----------------
boost-1.64.0 | py36_4 331 KB conda-forge
jemalloc-5.1.0 | hfc679d8_0 8.2 MB conda-forge
boost-cpp-1.64.0 | 1 17.8 MB conda-forge
salmon-0.10.2 | 1 3.7 MB bioconda
conda-4.5.5 | py36_0 624 KB conda-forge
tbb-2018_20171205 | 0 1.2 MB conda-forge
------------------------------------------------------------
Total: 31.8 MB

The following NEW packages will be INSTALLED:

boost: 1.64.0-py36_4 conda-forge
boost-cpp: 1.64.0-1 conda-forge
jemalloc: 5.1.0-hfc679d8_0 conda-forge
salmon: 0.10.2-1 bioconda
tbb: 2018_20171205-0 conda-forge

The following packages will be UPDATED:

conda: 4.5.4-py36_0 conda-forge --> 4.5.5-py36_0 conda-forge

Proceed ([y]/n)? y

Downloading and Extracting Packages
boost-1.64.0 | 331 KB | ####################################################################################################################################### | 100%
jemalloc-5.1.0 | 8.2 MB | ####################################################################################################################################### | 100%
boost-cpp-1.64.0 | 17.8 MB | ####################################################################################################################################### | 100%
salmon-0.10.2 | 3.7 MB | ####################################################################################################################################### | 100%
conda-4.5.5 | 624 KB | ####################################################################################################################################### | 100%
tbb-2018_20171205 | 1.2 MB | ####################################################################################################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

JRF @ MANIT

Sun, 02 Feb 2014 03:07:58 -0600

MAULANA AZAD NATIONAL INSTITUTE OF TECHNOLOGY BHOPAL

No. CSE/14/1038

Walk in Interview for the post of JRF under TEQIP-II

SN Department – Qualification Post Graduation – Time

1 Bio-Informatics & Mathematics M.Tech Bio-informatics/M.Sc.* Maths 10.00 AM

2 Biological Sciences M.Sc.* in any branch of Biological Sciences 10.30 AM

3 Chemical Engineering M.Tech Chemical Engineering 11.00 AM

4 Chemistry M.Sc.* Chemistry 11.30 AM

5 Civil Engineering M.Tech Structure/GeoTech. /Water -Resources/Hydraulics/Environment/Transport 12.00 Noon

6 GIS M.Tech GIS/Civil 12.30 PM

7 Computer Science & Engineering M.Tech CSE/Information Security 01.00 PM

8 Electrical Engineering M.Tech Electrical Derives 01.30 PM

9 Electronics & Communication M.Tech Digital Communication 02.00 PM

10 MSME M.Tech Material Science/ Mechanical/Metallurgy 02.30 PM

11 Physics M.Sc.* Physics 03.00 PM

* M.Sc. with NET/GATE qualified

Resume along with one passport size photograph and relevant documents are required at the time of interview

Amount of Fellowship: Rs 18000/-month+ HRA

Duration: 31st Dec 2014 (End of TEQIP-II project)

Date of Interview: 7th February 2014

Venue Institute Committee Room

http://www.manit.ac.in/manitbhopal/Year2014/Recruitment/Advertisement%20JRF.pdf

nanofilt: Filtering and trimming of long read sequencing data

Jit — Mon, 30 Jul 2018 12:01:52 -0500

Filtering on quality and/or read length, and optional trimming after passing filters.
Reads from stdin, writes to stdout.

Intended to be used:

directly after fastq extraction
prior to mapping
in a stream between extraction and mapping

https://github.com/wdecoster/nanofilt

Address of the bookmark: https://github.com/wdecoster/nanofilt

Post doc in Computational Genetics and Genomics at CEINGE Biotecnologie Avanzate, Naples, Italy

Tue, 11 Feb 2014 08:06:47 -0600

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

nQuire: a statistical framework for ploidy estimation using next generation sequencing

Jit — Thu, 04 Oct 2018 05:23:59 -0500

nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder

New version of Modeller, 9.13

Radha Agarkar — Thu, 13 Feb 2014 09:07:57 -0600

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.

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/

AMStat: display statistics of large sequence files from next generation sequencing projects

Neel — Fri, 09 Nov 2018 13:34:56 -0600

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.

Address of the bookmark: http://samstat.sourceforge.net/

The Best Bioinformatics / Computational Biology Quotes

Jit — Wed, 26 Feb 2014 17:50:59 -0600

Bioinformatician are not anti-social; We are just genome friendly.

Bioinformatician would love to change the biological world, but they won't give us the genetic code :P

If at first you don't succeed; call it version 1.0

The glass is neither half-full nor half-empty: it's actually have several genomes.

I'm BioGeek.

Fedup with LIPS, try God script.

Idiot, Go ahead, make my data!

Thank god, my genome just compiled.

Error message: "Out of space on genome drive:"

Shut up mobile elements, or i'll flush you out.

Never underestimate the internet bandwidth, u gotta incomplete.

Applied fuzzy logic to understand God's logic?

Warning! Overflow, delete chromosome !

Be nice to the BioGeek, for all you know they might be the next curator!

Beware of computational biologist they screw genes and protein.

Warning! Your genome is full of garbage, delete it !

Bad or missing mouse genome. Spank the cat? (Y/N)

Genome make very fast, very accurate mistakes.

Let's BLAST it.

Some genome never has transposons. It just develops random features.

Go watch CINEMA and have BLAST.

Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets

Neel — Sat, 06 Jul 2019 13:56:10 -0500

Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them.

Developper: Gaëtan Benoit, PhD, former member of the Genscale team at Inria.

Contact: claire dot lemaitre at inria dot fr

Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets. https://gatb.inria.fr/software/simka/

Address of the bookmark: https://github.com/GATB/simka