https://github.com/jennomics/WorkflowPaper/blob/master/Genome%20Assembly%20and%20Annotation.md

Address of the bookmark: http://bioinformatics.uconn.edu/bacterial-genome-assembly-tutorial/

www.cytosolve.com

Post - System Biologist

Job Description: Role of system biology is to design quantitative models of bimolecular networks and to study interactions between the components of biological systems, and how these interactions give rise to the function and behavior of that system (Enzyme, metabolites and pathway).

Qualification : B.Tech or M.Sc in Bioinformatics

Required Skills:

1) Basic knowledge of cell signaling pathways, chemical/enzyme kinetics, and differential equation based modeling approach.
2) Previous laboratory experience could be an advantage
3) Good Communication skills.

santhiya.ram@mproductions.com and 044-42946555.

It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. 

Address of the bookmark: https://github.com/tseemann/barrnap

A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630 004 on 03.08.2013 (Saturday) at 12:30 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.

1. Studentship (One Post):

Stipend : Rs. 5000 p.m. (consolidated)

Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/
Life Sciences

Interested candidates are encouraged to send their Curriculum Vitae by email to alagappauniv.btisnet@nic.in in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&DA will be given for attending the interview.

Advertisement: http://www.alagappabiotech.org/Notification.pdf

JRF/SRF / Project Assistant-II recruitment in National Agri-Food Biotechnology Institute (NABI)

Essential Qualification: According to the DST (DST OM No.SR/S9/Z-09/2012 dated 21.10.2014) Post Graduate degree in basic science(M.Sc) in Bioinformatics/Computational Biology/Systems Biology/Information Technology with NET or Graduate degree in professional course with NET or Post Graduate Degree (M.Tech) in professional course in Bioinformatics/Computational Biology/Systems Biology/Information Technology. Desirable qualification/skills: 1) Should be proficient in programming in Perl/Python/R language etc. 2) Should have knowledge and skills for data mining in biological sequence database . sequence analysis tools/packages, NGS Analysis . 3) Should have knowledge and skills to work in linux environment and write shell scripts.

Age : 28 years

Hiring Process : Written-test
Job Role : Research/JRF/SRF
How to apply

Application should be sent to Administrative officer, National Agri-Food Biotechnology Institute, Knowledge City, Sector-81, Mohali so as to reach latest by 30.05.2017 before 5:30 pm.

More at http://www.nabi.res.in/Vacancies/NABI/ResearchFellowships/JRFSRFRA/2017/ADVT.%20No%202017Researcher%20(02)/ApplicationForm.pdf

The most common newbie questions are:

Should I try to use these free open source programs?  Why are we not trying GUI software for computational analysis? Should I use commercial bioinformatics programs/software?”

1. Let’s be open

We generally think free and cheap are useless. But this concept is not applicable when we discuss open source software. Mostly, the bioinformatics software is developed by highly competitive biological programmers who believe in open sharing of knowledge. They come under Open Bioinformatics Foundation or O|B|F which is a non-profit, volunteer run organization focused on supporting open source programming in bioinformatics. The best part about open source tools/software is that they’re free to download the source code and read exactly what the program does. If you are so inclined, you can view all of the parts of the program and see the logical flow of the pipeline. In addition, open source makes an excellent learning tool for any beginning bioinformatician. Moreover, you can modify existing open source programs to deal with cutting-edge problems or to customize your pipeline. Apart from your computational and analysis work, most of the reviewer also prefers the open source based results so that they can validate the results if validation required.

2. Code headache

As a bioinformatician you are supposed to know the basics of programming languages, and if you are not good at it, then please learn it as soon as possible because you are not a bio-analyst but biological programmers. The open source programs usually lack dedicated service and support teams (often because they were the product of an overworked doc/postdoc!) so you are responsible for troubleshooting your own errors most of the time. We commonly receive the HELP email to support and assist to setup the pipeline; you can also find this kind of request on any QA forum. I personally believe this coding horror brings the biggest downside of open-source programs; where you need some programming skills in order to implement the program in your pipeline. But, if you are not able to fix the pipeline and modify the open source code according to your requirements them you should re-think on your bioinformatician name tag!!!

3. Dive into the codes

Some of the biologist turn bioinformatician says “if you can do the same thing with commercial software then why to get migraine with weird codes”, well this statement looks to me that guys are keen to learn swimming but still don’t like to get wet. If you are still using paid software and doing your work by customer support and clicking some of the well-designed GUI button then perhaps you are not interested in learning and trying new and challenging bioinformatics works. You are missing the basic flavour of bioinformatics. Let’s dive into the coding world, I am sure your will enjoy it. I recommend your to swim freely in code’s sea, and enjoy the journey; do not merely watch it from the outside.  

4. Paid does not mean better

The bioinformatics company which are specializes in bioinformatics solutions develop well designed/packed, user friendly software by using a large number of specialised scientist, programmers and support staff. They also provide good services to accomplice your biological analysis work. This means that if you hit a ‘snag’ with your data, help is likely only a phone call away! These companies price their products competitively against the cost of a dedicated bioinformatician. You may be able to afford the program, but not the additional staff! Additionally, most of the functionality that you need in your analysis is already coded into the program. Need to plot a graph? Just click this button right here. It is that easy. But, as a bioinformatician this is not generally well encouraged approach in biological analysis work, because the software is not available to everyone and your data can’t be validated. Moreover, there is very less chances that anyone will repeat your work or love to do similar kind of research (because not all the labs in the world are rich like yours).

5. Take a caution

In biological analysis work, in which you deal GB/TB of data are having maximum chances of getting errors, so please be careful and always cross check your data before coming to any conclusion. Even an error in two line code can alter your entire analysis and display weird results. Some of the scientist blindly believes on commercial software, which is entirely wrong. Using proprietary tools does not absolve you of the need to actually read and research the type of analysis that you are doing. This is particularly true in the case of genome assembly and annotation.

At the end, I would like to tell only one think that open source solutions allows you to do more cutting edge analysis than the commercial tools. So let’s go for it.

Disclaimer:

This is my personal view. I have nothing to do with any company or open source community. The views expressed on these pages are mine alone and not those of my current/past employers. I do reserve the right to remove comments left by spammers or off-topic comments.

http://www.disi.unige.it/person/MasulliF/ricerca/PhDinGenova2017.html

The call for some funded positions for the 3 years PhD studies at the Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS) in Genova is available at

http://www.studenti.unige.it/postlaurea/dottorati/XXXIII/ENG/

The deadline for applications is June13, 2017 and the PhD courses and fellowships should start on Nov 2017.

Details for the application to the PhD Program in Computer Science and Systems Engineering (CODICE 6608) are at http://phd.dibris.unige.it/csse/index.php/how-to-apply

The research activity of my research group is focused on Computational Intelligence, Machine Learning, Bioinformatics, Systems Biology, and Positive Technology as described at http://www.disi.unige.it/person/MasulliF/ricerca/index.html

The research themes proposed by me and Prof. Stefano Rovetta are:

- Computational Intelligence and Machine Learning (see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T1.html)

- Computational Intelligence and Health and Wellbeing Support( see http://www.disi.unige.it/person/MasulliF/ricerca/Phd2017-T3.html)

You can also propose a different research theme belonging to the research activity of my group.

Looking for self-motivated PhD candidates, interested to the mathematical aspects of their research and to the development of new algorithms for intelligent data analysis, and skilled in programming and in thorough experimental data analysis. They will be part of my research group and will collaborate to our research projects and publications.

Italian and international students interested to work are invited to send their cv and the name/email-addresses of 3 referees to my email address francesco.masulli@unige.it A.S.A.P.

Genomics England will play a key role in building on the UK’s long track record as leader in medical science advances to push the boundaries by unlocking the power of DNA data. The UK will become the first ever country to introduce this technology in its mainstream health system – leading the global race for better tests, better drugs and above all better, more personalised care.

http://www.genomicsengland.co.uk/100k-genome-project/

Advertisement No. 137/ESTB/NIBMG/17-18

Position available Project Description: Several positions are available for the project titled: “A unified web-portal for analysis, integration and visualization of multi-omics data”. The goal of this project is to develop a user-accessible resource for integrated analysis and visualization of multi-OMICs data sets (including gene expression, genotype, methylation, microRNA, etc.). Data sets generated on various platforms shall be maintained in a stable database, accessed through standard querying mechanisms, and the results shall be displayed via user-friendly interface. The analysis engine shall run on open-source software (such as R/Bioconductor) developed in-house. All positions are contractual.

Appointment will be initially given for a period of one year which is extendable depending upon performance, availability of funds and requirements of the institute.

Project Code: 20275 Position: (No. of positions available)

Research Associate (3)

Position 1: Ph.D. or equivalent in statistics, computer science, mathematics, bioinformatics, or related subject.
Position 1: Those with experience in database management shall be preferred. Experience with UNIX or GNU/Linux operating system.
Position 1: Creation and maintenance of a database for population- and diseaseassociated variation resource. Development of programmatic interface for querying the database, filtering of the results and identification of genes of interest.

Rs. 36000/- + 10% HRA

Please apply online via web link http://apply.nibmg.ac.in/ (no other form of application will be accepted). The last date of application is 14-08-2017. All letters to attend screening test and /or interview will be sent only to the short-listed candidates by Email only. No correspondence will be made with applicants who are not shortlisted /not called for screening test and /or interview. No TA/DA will be paid for attending the screening test and /or interview.
Detail information at http://www.nibmg.ac.in/academic/Advt_20275.pdf

More Info: http://www.nibmg.ac.in/?q=Project%20Linked%20Personnel

SciGenom Research Foundation (SGRF) and Institute of Genomics and Integrative Biology (IGIB) are pleased to host the Next-Generation Sequencing and Bioinformatics for Genomics & Healthcare conference.

In the ten years since the first human reference genome was completed for US$3 billion the sequencing technologies have radically changed leading to great reduction in sequencing cost. Today a human genome can be sequenced for under US$ 5000 in less than two weeks. It is expected that by the end of 2015 the cost of sequencing a human genome will drop to below thousand dollars. The next generation sequencing technologies over the past five years have enabled a large number of genomic studies that impact human health and disease. Also, this has made possible the growth of microbial, animal and plant genomics studies. While the data production has increased at a rapid pace challenges remain in analyzing and understanding the data. The conference will cover the next generation sequencing (NGS) technologies, bioinformatics for NGS and applications of NGS in many areas including personalized medicine.

For more info : http://www.scigenomconferences.com/2013/default.php