<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/28290?offset=720 https://bioinformaticsonline.com/bookmarks/view/38535/nanopack-visualizing-and-processing-long-read-sequencing-data Tue, 25 Dec 2018 21:20:50 -0600 https://bioinformaticsonline.com/bookmarks/view/38535/nanopack-visualizing-and-processing-long-read-sequencing-data <![CDATA[NanoPack: visualizing and processing long-read sequencing data]]> Address of the bookmark: https://github.com/wdecoster/nanopack

]]> Jit https://bioinformaticsonline.com/opportunity/view/8123/jrf-manit Sun, 02 Feb 2014 03:07:58 -0600 <![CDATA[JRF @ MANIT]]> 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

Advertisement:

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

]]> 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/bookmarks/view/40754/understanding-your-reads-and-mapping Wed, 29 Jan 2020 06:29:55 -0600 https://bioinformaticsonline.com/bookmarks/view/40754/understanding-your-reads-and-mapping <![CDATA[Understanding your reads and mapping !]]> One of the best tutorial for beginners ...

https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Address of the bookmark: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

]]> Neel 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.

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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/bookmarks/view/34470/simngs-and-simlibrary-%E2%80%93-software-for-simulating-next-gen-sequencing-data Tue, 28 Nov 2017 06:49:11 -0600 https://bioinformaticsonline.com/bookmarks/view/34470/simngs-and-simlibrary-%E2%80%93-software-for-simulating-next-gen-sequencing-data <![CDATA[simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data]]> simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from more esoteric sources of noise that may be present in real data ("dust", bubbles, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied.

simNGS takes fasta format sequences and a file describing the covariance of noise between bases and cycles observed in an actual run of the machine, randomly generates noisy intensities representing the signals for the sequence at each cycle and calculates likelihoods for all possible base calls.

Address of the bookmark: https://www.ebi.ac.uk/goldman-srv/simNGS/

]]> Jit https://bioinformaticsonline.com/fun/view/8509/the-best-bioinformatics-computational-biology-quotes Wed, 26 Feb 2014 17:50:59 -0600 https://bioinformaticsonline.com/fun/view/8509/the-best-bioinformatics-computational-biology-quotes <![CDATA[The Best Bioinformatics / Computational Biology Quotes]]> image

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.

]]> Jit https://bioinformaticsonline.com/blog/view/8987/the-dna-of-a-successful-bioinformatician-decoded Wed, 12 Mar 2014 13:41:26 -0500 https://bioinformaticsonline.com/blog/view/8987/the-dna-of-a-successful-bioinformatician-decoded <![CDATA[The DNA of a Successful Bioinformatician decoded !!!]]> Many blogs exist about successful bioinformatician, but this blog so far now is my personal view on characteristics of successful bioinformatician or computational biologist.  Hmm … of course these views are subjective to my own personal experiences and therefore I don't claim that the view listed here is complete. As a human, I don’t take them too serious. The success must not be the only target of your work. The target is to work on your own virtues; some of those virtues are the topic of this blog.

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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!

]]> Jit https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 Fri, 07 Jul 2017 04:06:59 -0500 https://bioinformaticsonline.com/pages/view/33837/awesome-perl-frameworks-libraries-and-software-part-1 <![CDATA[Awesome perl frameworks, libraries and software - PART 1]]> A curated list of awesome Perl frameworks, libraries and software.

]]> Neel https://bioinformaticsonline.com/bookmarks/view/34461/drawid-user-friendly-java-software-for-chromosome-measurements-and-idiogram-drawing Mon, 27 Nov 2017 16:03:49 -0600 https://bioinformaticsonline.com/bookmarks/view/34461/drawid-user-friendly-java-software-for-chromosome-measurements-and-idiogram-drawing <![CDATA[DRAWID: user-friendly Java software for chromosome measurements and idiogram drawing]]> "DRAWID has number of advantages including a user-friendly interactive interface, possibility for simultaneous chromosome and FISH/GISH/banding signal measurement and idiogram drawing as well as number of useful functions facilitating the procedure of chromosome analysis," explain the scientists.

"The output of the program is Microsoft XL table and publish-ready idiogram picture."

Find their paper openly published with us at: https://doi.org/10.3897/compcytogen.v11i4.20830

Address of the bookmark: https://compcytogen.pensoft.net/articles.php?id=20830

]]> Robert M Willioms