The fate of a cell is ultimately the product of the regulation of its genes. Gene regulation is a coordinated process acting at multiple levels of which transcription and translation are the most prominent. The Valen group is dedicated to the fundamental question of how transcription and translation is integrated to obtain the desired protein abundance. The recent development of high-throughput next generation sequencing techniques to monitor both active translation and transcription has made it possible to study this connection at the genome scale.

This project aims to elucidate the links between regulation of translation and transcription. The applicant will analyze next generation sequencing data and model gene regulation on a genome-wide level to identify the features that affect the translational output of transcripts. The work will be done in close collaboration with experimental scientists who will test the predictions of the computational models.

Additional information on the position can be obtained by contacting Eivind Valen (eivind.valen@ii.uib.no).

The research fellow must take part in the University’s approved PhD program leading to the degree within a time limit of 3 years. Application for admission to the PhD program, including a project plan outline for the training module, will be worked out in collaboration with the research group in question.

In total, the fellowship period is 4 years, 25 % of this will be allocated to teaching and/or administrative duties. The fellowship period may be reduced if the successful applicant has held previous employment as a research fellow or similar.

http://www.jobbnorge.no/en/available-jobs/job/102235/research-fellow-phd-candidate-in-computational-biology-2-positions

1. NCBI (National Center for Biotechnology Information):

   • NCBI provides various databases related to genetic information, including 16S rRNA sequences.
   • You can access the 16S ribosomal RNA sequences from NCBI's Nucleotide database (https://www.ncbi.nlm.nih.gov/nucleotide/).
   • Perform a search using keywords like "16S rRNA" or specific bacterial names to find relevant sequences.
   • You can download sequences individually or in batches using the provided tools.

2. GreenGenes:

   • GreenGenes is a widely used 16S rRNA gene sequence database.
   • You can access it at http://greengenes.secondgenome.com/.
   • GreenGenes provides precompiled databases for various purposes, including classification, alignment, and phylogenetic analysis.

3. SILVA:

   • SILVA (https://www.arb-silva.de/) is another comprehensive database for ribosomal RNA (rRNA) sequences.
   • It covers not only 16S rRNA but also other ribosomal RNA sequences.
   • SILVA provides precompiled databases for various purposes, including taxonomic classification and alignment.

4. Ribosomal Database Project (RDP):

   • RDP (http://rdp.cme.msu.edu/) is a curated database that offers 16S rRNA sequences.
   • It provides tools for sequence analysis and classification.
   • You can download sequences and taxonomy information from their website.

5. QIIME (Quantitative Insights Into Microbial Ecology):

   • QIIME (https://qiime2.org/) is a widely used bioinformatics platform for microbiome analysis.
   • It provides tools for analyzing microbial communities, including processing 16S rRNA sequences.
   • QIIME often includes its own preprocessed 16S rRNA databases that can be used for analysis within the platform.

Before downloading any database, make sure to read the terms of use and citation requirements, as some databases may have specific usage policies. Additionally, consider the compatibility of the database with your analysis pipeline and software tools.

NCBI 16s RNA database location ftp://ftp.ncbi.nih.gov/blast/db/16SMicrobial.tar.gz

1. Make friends with local bioinformatics groups
2. Talk to your computing group
3. Obtain clear expectations
4. Rewrite your job description
5. Papers
6. Attend bioinformatics meetings
7. Try first, ask later

Address of the bookmark: http://biomickwatson.wordpress.com/2013/04/23/a-guide-for-the-lonely-bioinformatician/

To understand the evolution of the biodiversity seen on planet earth is one of the major goals in biology. How animals explored new habitats from only being confined to the marine environment and the how the forms diversified is still one of the most tremendous questions to be answered.

http://www.sars.no/research/HejnolGrp.php

The Job detail

Advancing the SNP-discovery and polymorphism assessment work across several germplasm panels representing global genetic diversity
Population genetic and genomic analyses, testing the hypothesis related to adaptation in multiple geographic regions
Develop SNP assays from large scale GBS and other re-sequencing data for several target traits utilizing available phenotyping data
Combined analyses of genotypic and phenotypic data for discovery of marker-trait associations, and conducting GWAS
Processing, analyzing, and archiving large-scale genomic data sets, assessing data quality, conducting analyses, interpreting findings, and communicating findings to others including preparation of reports, presentations, posters and journal articles
Providing support to MSc and PhD students on topic related to its major core of research
Any other work assigned by the supervisor

The Person:

PhD in bioinformatics, genetics, computational biology preferably with 1 to 2 years of experience;
familiar with standard bioinformatics tools and scripting languages and emerging and evolving software platforms relevant to bioinformatics and computational biology;
ability to create new analytical pipelines; experience with handling large data sets;
ability to program in at least two of the following: C++, PERL, Python, R, Java.
will use next-generation sequencing technologies to generate marker data for genetic mapping and transcriptome data for expression QTL mapping, and will be responsible for data generation as well as data analysis.

Period and Remuneration: The assignment is for a period of two years, and can be extended for another year depending on performance. ICRISAT pays a very attractive all inclusive lump sum assignment fee payable in Indian Rupees.

How to Apply: Please send your application by email to icrisatjobs@cgiar.org, stating the job title (Special project Scientist-Sorghum Genomics) clearly in the subject column, addressed to the Director, Human Resources and Operations, ICRISAT, Patancheru, Andhra Pradesh 502 324, India, latest by 10 June 2014. The application should include an up-to-date Curriculum Vitae, a short statement of competencies and experience for the position, and the names and addresses (including phone/e-mail) of three referees. Only short-listed candidates will be contacted.

More at: http://www.icrisat.org/careers/Special-Project-Scientist-Sorghum-Genomics.htm

• Homology-based misassembly correction
• Homology-based assembly scaffolding and patching
• Scaffold merging

Address of the bookmark: https://github.com/malonge/RagTag

Webpage : https://www.scilifelab.se/about-us/
Opportunity: https://www.scilifelab.se/about-us/career/

In comparative genome analysis work, we usually compare more than two genomes and looks for syntenic regions amongst them. In my research I used Evolution Highway (RH) http://eh-demo.ncsa.uiuc.edu/, which is a collaborative project designed to provide a visual means for simultaneously comparing genomes of multiple amniote species. The tool removes the burden of manually aligning these maps and allows cognitive skills to be used toward something more valuable than preparation and transformation of data. In addition to EH, attractive Circos (http://circos.ca/) is also very popular for this kind of analysis.

The EH is available online, and can be easily access and use, whereas Circos installation is not entirely straightforward. One of the most difficult parts of the installation involves installing the GD library. Since there weren't good instructions for installing this library on the internet I decided to post instructions here in case they are useful to anyone else.

Following are the steps to install GD modules in Mac OS

1. Setup

Create a folder for the files:

$ mkdir -p /SourceCache
$ cd /SourceCache

Get and unpack the required Jpeg-6b and GD libraries:
Download Jpeg-6b (http://code.google.com/p/google-desktop-for-linux-mirror/downloads/detail?name=jpeg-6b.tar.gz&can=2&q)
Download GD (http://search.cpan.org/~lds/GD-2.46/)

Place the "tar.gz" files in "/SourceCache" and double click to unpack.

2. Install libjpeg

Copy the "config.sub" and "config.guess" files to "/SourceCache". Note that your "config.sub" and ""config.guess" files may be in a slightly different location. The commands below show where they were on my machine:

$ cd /SourceCache/jpeg-6b/src
$ cp /usr/share/libtool/config/config.sub .
$ cp /usr/share/libtool/config/config.guess .

Configure libjpeg as follows. Note that this was installed on a 64 bit machine. However, this method may configure it in a 32 bit format. This may not be the best way to configure the installation but it works.

$ .configure --enable-shared
$ make

Check to see if the following directories exist on your machine. Create the missing directories in the following manner:

$ mkdir -p /usr/local/include
$ mkdir -p /usr/local/bin
$ mkdir -p /usr/local/lib
$ mkdir -p /usr/local/man/man1

Finish making and installing libjpeg:

$ make install

3. Install GD

$ cd /SourceCache/GD-2.46/GD/
$ perl Makefile.PL
$ make
$ make test (optional)
$ make html (optional)
$ make install

Other way for Mac OS
The easiest way to get a lot of these is with a program called Fink, which is similar in nature to the CPAN installer, but installs common GNU utilities. Fink is available from <http://sourceforge.net/projects/fink/>.

Follow the instructions for setting up Fink. Once it's installed, you'll want to run the following as root: fink install gd

It will prompt you for a number of dependencies, type 'y' and hit enter to install all of the dependencies. Then watch it work.

To prevent creating conflicts with the software that Apple installs by default, Fink creates its own directory tree at /sw where it installs most of the software that it installs. This means your libraries and headers for libgd will be at /sw/lib and /sw/include instead of /usr/lib and /usr/local/include. Because of these changed locations for the libraries, the Perl GD module will not install directly via CPAN, because it looks for the specific paths instead of getting them from your environment. But there's a way around that :-)

Instead of typing "install GD" at the cpan> prompt, type look GD. This should go through the motions of downloading the latest version of the GD module, then it will open a shell and drop you into the build directory. Apply below patch to the Makefile.PL file (save the patch into a file and use the command patch < patchfile.)

Then, run these commands to finish the installation of the GD module:

perl Makefile.PL
make
make test
make install
And don't forget to run exit to get back to CPAN.

Install on MS Window, using PPM

C:\Documents and Settings\Owner>ppm
PPM interactive shell (2.2.0) - type 'help' for available commands.
PPM> install GD
Install package 'GD?' (y/N): y
Installing package 'GD'...
Downloading http://ppm.ActiveState.com/PPMPackages/5.6plus/MSW. ...
Installing C:\Perl\site\lib\auto\GD\GD.bs
Installing C:\Perl\site\lib\auto\GD\GD.dll
Installing C:\Perl\site\lib\auto\GD\GD.exp
Installing C:\Perl\site\lib\auto\GD\GD.lib
Installing C:\Perl\html\site\lib\GD.html
Installing C:\Perl\site\lib\GD.pm
Installing C:\Perl\site\lib\qd.pl
Installing C:\Perl\site\lib\auto\GD\autosplit.ix
PPM>


If you can't install it from ppm. You can download it:
http://ppm.ActiveState.com/PPMPackages/5.6plus/MSW.


BTW,All Perl 5.6.1 Modules are located at:

http://ppm.ActiveState.com/PPMPackages/5.6plus/MSW.

Install the Perl GD Module on Linux

$ sudo perl -MCPAN -e shell

Since it was the first time I had run this command on this particular machine I had to answer a lot of questions but simply selected the defaults for everything as this usually works for me. Once in the CPAN shell I entered

$ install Bundle::CPAN

and selected all of the defaults again. Once the CPAN bundle had finished installing I tried to install GD::Graph by typing

$ install GD::Graph

but it failed with hundreds of errors – the first of which was

GD.xs:7:16: error: gd.h: No such file or directory

This was fixed with the following apt-get command (in the bash shell)

$ sudo apt-get install libgd2-xpm-dev

back in the CPAN shell I still couldn’t get GD::Graph to build and I guessed this was because of some left over files from the failed build. I don’t know the command to clean things up inside the CPAN shell and am too lazy to read the docs so I simply went into the .cpan/build directory in my home directory and deleted anything that started with GD – eg

$ rm -rf GD-2.35-HC_vkB

$ rm -rf GDGraph-1.44-Evfibe

and so on. Those strings at the end (VkB and so on) look random so they might be different on your machine. Then I went back into the CPAN shell and ran

$ install GD::Graph

There were a few dependencies which the script fetched and installed for me but everything worked smoothly.

Manual and other Perl Module instalation are mentioned in my previous blog @ http://bioinformaticsonline.com/blog/view/710/how-to-install-perl-modules-manually-using-cpan-command-and-other-quick-ways

Walk- in- Test cum Interview (based on test) for the selection of Research Associate

under the scheme “Distributed Information Sub Centre –DISC” & Research Assistant under scheme “Phytophthora, Fusarium and Ralstonia diseases of Horticultural and Field Crops” will be held at this Institute as per details indicated below.

WALK -IN- TEST CUM INTERVIEW

Name of the post : Research Associate

Date of Interview : 21-05-2014 at 10.00 AM

No. of posts : One

Qualifications : a)Essential

Ph.D Degree in Bioinformatics OR : Masters degree in Bioinformatics with a minimum of
60% marks or equivalent OGPA with at least two years research experience as evidenced from fellowship/ associateship/training/published papers etc.

b)Desirable: Experience in NGS data analysis.

Emoluments : Rs. 23,000/- per month + HRA (Masters Degree Holders)

Rs. 24,000/- per month + HRA (Ph.D Degree Holders)

Upper age limit : 40 years for Men & 45 years for Women as on date of Interview (Upper Age limits are relaxable for SC, ST and OBC candidates as per Govt. of India norms (at present 5 years for SC/ST and 3 years for OBC)

Duration of Project : Till 31-03-2017.

Title of Assigment : Research Assistant (on contract basis)

No. of vacancy : One

Qualification : Essential : Post Graduation in Bioinformatics and Minimum one year experience in NGS data analysis

Desirable : Experience in Perl/Python/R

Remuneration : Rs. 20,000/- per month (consolidated)

Scope of work :

1. Analysis of different file formats and their conversions.

2. Assessing the quality of data and filtering of raw reads.
3. Assembling the raw reads-de novo as well as reference mapping.
4. Compression of aligned reads using Jam tools
5. RNA-seq. Analysis
6. Differential expression testing involving Normalization, Statistical testing, heat map generation & hierarchical clustering
7. Annotating the assembled genome and geneet testing and their validation
8. Metabolic pathway analysis
9. Comparative genomics
10. Setting up of genome browsers.

Period of Assigment : Initially for six months.

Date & Venue of Interview : 21-05-2014 at IISR, Kozhikode at 10.00 AM

More at http://www.spices.res.in/pdf/disc-advtmnt.pdf

Address of the bookmark: http://www.citrusperl.com/