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

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

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/

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

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.

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

1. Update new things continuously
As per my personal experience, it’s not always easy to work as a bioinformatician!  There are couple of reasons to say that; First computational part of biology make our life’s a little harder compared to other professional categories. The fact - for instance - that the technology cycle in the bioinformatics world is very short, the actual knowledge becomes outdated in a few months or years. Therefore, we need to learn continuously - new things get important. Second, to stay on top of things we really need the strong will to be good at our job. That's probably the most important characteristic to bioinformatician. They are usually an excellent knowledge worker with great technical abilities, and have the will to be that over decades!

2. Avoid the sentence "I did not know what to do!"
In our computational biology lab, we generally face lots of technical problems. But as you know, it's impossible to know everything to do the computational biology jobs ( Yup.. because you need diverse and multidisciplinary knowledge to understand biological problems and resolve their respective solutions), therefore it's absolutely necessary that a bioinformatician finds its way through a new topic. How I typically do that is I use google and I talk to other experts in our laboratory or online biostar community to find out what they think. "I did not know what to do!" should not be an argument for us.

3. To make oneself useful
Several time it does happen, you finished our task earlier than expected; in such cases if you have some time left then: Take a coffee and play chess; reversi, etc. In my case I take a rest. Afterwards I think about what I could do that helps the team to achieve its targets, 'cause some of my team mates probably didn't finish! (at least if I didn't met them at coffee bar !!)

4. Care for all
During my rigorous research duration; I attended several workshop organized by my University departments. I had a discussion with other research fellow, professors; I generally ask … what it really takes to make a team successful or to be a successful research leader. They always said: "Well, you need some caring people!" I think there is a lot truth in that statement. If we do not care about quality, timelines, good team culture, respectful communication (!!), clean code, if all this doesn’t matter to us, then I believe the probability is higher that we fail in research and analysis.

5. Be good with people
Because bioinformatician and computational biologist jobs typically involves to work in a (most wanted J cross-departmental!) team, therefore it's important that we're (more or less) good in dealing with other individuals. Everyone have their own strengths and weaknesses, just like us. It's important to treat all the research team mates with respect, regardless of their technical competence or contributions. Of course, sometimes people deserve a clear statement (!!!), but try to do these things one-on-one. Make sure nobody loses his face. Attend the meetings at the coffee bar; be good at table top soccer and go out once in a while to have a beer with your team. You know what I'm talking about.

At the end of a week I look back and I ask myself what I have produced. This could be paperwork, community days or (best!!) programming code. Always remember there is always a solution to a problem. Most of the times there are at least three solutions. So, don’t just blame, suggest a solution.

That's it. I am looking forward to your thoughts and comments!

https://www.researchgate.net/job/939073_Senior_Scientist_Bioinformatics-Multi_Omics_Integration

Senior_Scientist_Bioinformatics-Transcriptomics_Analysis

https://www.researchgate.net/job/939075_Senior_Scientist_Bioinformatics-Transcriptomics_Analysis-Belgium_France_Switzerland_The_Netherlands

Senior Scientist Bioinformatics - Network Analytics

https://www.researchgate.net/job/939070_Senior_Scientist_Bioinformatics-Network_Analytics_Belgium_France_Switzerland_the_Netherlands

Team Leader Bioinformatics Data Sciences - Mechelen, Belgium

https://www.researchgate.net/job/938787_Team_Leader_Bioinformatics_Data_Sciences-Mechelen_Belgium

For knowledge about Linux and their importance amongst bioinformatician plesae read this article "An introduction to Linux for bioinformatics" by Paul Stothard.

Linux cheat sheet at http://bioinformaticsonline.com/file/view/87/linux-cheat-sheet

Please browse for futher useful linux pages on right hand side ...

1. Illumina, Inc. (U.S.)

Illumina, Inc. was founded in 1998 and is headquartered at San Diego, U.S. Illumina, Inc. is one of the leading players in DNA sequencing and array-based technologies, serving customers in the research, clinical, and applied markets. The company offers products for applications in the life sciences, oncology, reproductive health, agriculture, and other emerging segments. The company serves government laboratories, genomic research centers, academics institutions as well as pharmaceutical, biotechnology, agrigenomics, commercial molecular diagnostics laboratories and consumer genomics companies. Illumina, Inc. has its geographic presence in North America, Europe, Latin America, Asia-pacific, and others.

2. QIAGEN N.V. (Netherlands)

QIAGEN N.V. was incorporated in 1986 and is headquartered at Venlo, The Netherlands. The Company is engaged in providing Sample to Insight solutions that transform biological samples into molecular insights. QIAGEN provides its workflow to customers in molecular diagnostics, assay technologies, bioservices and automation systems.  The company’s genome services are suitable for custom/tailored projects that allow access to genomic sequence information.  The Company market its products in more than 100 countries across the Americas, Europe, Asia, Australia, and the Middle-East &Africa through its subsidiaries and channel partners.

3. PerkinElmer, Inc. (U.S.)

PerkinElmer, Inc. was founded in 1947 and is headquartered in Waltham, Massachusetts, the U.S. PerkinElmer, Inc. offers its products & services and solutions for the diagnostics, food, environmental, industrial, life sciences research and laboratory services markets. The company offer comprehensive genetic testing solutions that help to provide insight into the complex nature of rare and inherited diseases. Some of the subsidiaries of the company are Caliper Life Sciences, Improvision, Viacell Inc., ViaCord LLC, among many others. The company has its facilities located in Europe (France, Germany, and Belgium), U.S. and Asia (China, India, and Japan).

4. Eurofins Scientific SE (Luxembourg)

Eurofins Scientific SE was founded in 1987 and is headquartered in Luxembourg, Europe. The company offers a portfolio of over 130,000 analytical methods and more than 150 million assays performed each year to establish the safety, identity, composition, authenticity, origin, traceability, and purity of biological substances and products, as well as carry out human diagnostic services. The company has its geographic presence across 39 countries in Europe, North and South America, and Asia-Pacific.

5. GATC Biotech AG (Germany)

GATC Biotech AG was founded in 1990 and is headquartered in Constance, Germany. The company provides DNA and RNA sequencing and bioservices solutions to academics and industrial areas. It also provides next generation sequencing services including genomes, targeted (re)-sequencing, human sample sequencing, transcriptomes, metagenomes, regulomes, pre-sequencing, NGS barcode labels, and next generation sequencing technologies; and bioservices services, including bioservices tools, pipelines and workflows, compute resources, data analysis reports, and case studies. GATC Biotech AG operates as a subsidiary of Eurofins Scientific SE. It offers its products through distributors in Italy, Japan, Portugal, Spain, and the Czech Republic.

6. Macrogen, Inc. (South Korea)

Macrogen, Inc. was founded in 1997 and is headquartered in Seoul, South Korea. Macrogen, Inc. provides next generation sequencing services such as whole genome, de novo, exome, targeted, transcriptomics, metagenome, and epigenome sequencing.  The company also provides a variety of services such as oligo synthesis, database construction, genome research, and bioservices analysis system consulting services. Macrogen, Inc. provides genome research services in Korea and internationally.

7. Genotypic Technology Pvt. Ltd. (India)

Genotypic Technology Pvt. Ltd. was incorporated in 1998 and is headquartered in Bangalore, India. Genotypic Technology is the first Genomics service provider in India providing Microarray, Next Generation Sequencing (NGS), Bioservices and solutions to domestic/ international pharma, biotech companies and academia. The company provides its services for protocol optimization, probe designing, array layouts, project designing, and nucleic acid analysis to in-depth analysis. Genotypic Technology has its geographic presence in North America, Europe, Asia Pacific, Middle East & Africa, and Latin America.

8. GENEWIZ, Inc. (U.S.)

GENEWIZ, Inc. was founded in 1999 and is headquartered in South Plainfield, New Jersey, the U.S.; The company is a leading provider of research service in the field of Next Generation Sequencing, Sanger DNA sequencing, sequencing of bacteria and phage, gene synthesis, DNA cloning, genomics including mutation analysis, single nucleotide polymorphism, and bioservices. GENEWIZ, Inc. has its geographic presence in U.S., China, Germany, France, Japan, and the U.K.

9. Beijing Genomics Institute (China)

Beijing Genomics Institute (BGI) is the world’s largest genomics organization and non-profit research institution that was founded in 1999 and is headquartered in Shenzhen, China. The Company provides a wide range of commercial next generation sequencing services and genetic tests for medical institutions, agricultural and environmental applications. The Company operates all across the globe through its subsidiaries, namely, BGI China (Mainland), BGI Asia Pacific, BGI Americas (North and South America) and BGI Europe (Europe and Africa).

10. SciGenom Labs Pvt. Ltd (India)

SciGenom Labs Pvt. Ltd was founded in 2010 and is headquartered in Cochin, India with offices in Chennai & Hyderabad in India, and San Francisco in the U.S. It is a Genomics R&D services company that provides genomic sequencing and NGS services to life sciences and healthcare businesses globally as well as academic and government institutions in India.

Popular mentions – MedGenome (India), DNA Link, Inc. (South Korea), Otogenetics Corporation (U.S.), Novogene Corporation (China), LGC Limited (U.K.), CD Genomics (U.S.), SeqLL, LLC (U.S.)