BOL: Related items

BioScripts

Rahul Nayak — Sun, 28 Jun 2015 07:46:14 -0500

You are requested to please bookmark collection of bioinformatics tools, scripts, codes that can be pieced together in a very easy and flexible manner to perform both simple and complex bioinformatics tasks.

The next-generation sequencing included whole genome sequencing(WGS), transcriptome sequencing (whole cDNA sequencing, RNA-seq), digital gene expression sequencing (Tag-Seq), ChIP-Seq, and so on. And there are many sequencing platform to generate sequece, as well know Sanger/ABi(the frist generation), Solexa/illumina, SOLiD/ABi, 454/Roche. But thier sequence format is different, also they have different error type. High quality data is very important for further analysis or data mining. There are many pipeline for raw sequence quality analysis and control with few of process for reporting reads quality statistical details, trimming, filtering, and error correction. Please bookmarks them for the benefits of bioinformatics community.

https://code.google.com/p/biowiki/

https://code.google.com/p/ngs-pipeline/source/browse/#svn%2Ftrunk

NGSand Perl scripts https://code.google.com/hosting/search?q=NGS+perl&projectsearch=Search+projects

NGS and Python scripts https://code.google.com/hosting/search?q=NGS+Python&projectsearch=Search+projects

Address of the bookmark: https://code.google.com/hosting/search?q=bioinformatics&sa=Search

Bioinformatics PhD / PostDoc / Job Rejection

Jit — Thu, 02 Jul 2015 08:52:46 -0500

While your PhD or PostDoc application, it is more common that you got rejected by many professors. Don't disappoint reply it calmly.

In grad school, I shared a house with three Bioinformatics PhD students. One, when he applied to a particular professor, received a letter that said, essentially, "If you are applying because you want to enrich yourself, great. If you are applying because you want a job, you should know that you won't get one." I am trying to tell you this is because if you, with a good background in Bioinformatics, are passing up opportunities, you must be a strong candidate in many areas. Enrich yourself.

So, my suggestion is take a deep breath, forgot about all. Don’t take it personally. It's been usual processes while hunting for a good lab and professor. Take is positive, I am not sure why they reject, but don't worry perhaps the lab don't deserve you. Always remember there are billions of reasons not to hire someone for projects, especially in a research sector.

My suggestion, please do not whine about how you were a great research candidate for the post, and you just can't understand why they were so stupid as to have rejected you! This feeling will not win you any points in research, community. Especially, when in todays socially connected era everyone is linked. Remember, a nice E-mail saying, "I really wished to working with you on this project and I hope we cross paths again," is all you need to send to the professor. Send a thank you note to the professor. Thank them for the time they spend to judge you. In the future, If you and the professor (of your dream) are attending a bioinformatics conference, invite him/her to lunch (please remember to pay the bill). In today evolving scientific ere, always remember to build your solid network in order to get a job of interest. Join all possible networking sites like LinkedIn, ResearchGate, Acamedia, FB for the same reason. You as a researcher always build a bridge with student/researcher/colleague/professor who have the research potential to lead in research and hire you. Just because you didn't get this project, doesn't mean there isn't another that will open up in couple of month.

Mostly, jobs that are hard to get are hard to get. Only you can decide if the continued sacrifices are worth the expected payout. If it is, keep on plowing. Build relationships. Attend conferences.

Image ref @ JaSonYa

SRF post in NEHU, Shillong

Tue, 04 Aug 2015 03:17:05 -0500

Bioinformatics Centre (DIC)
NORTH-EASTERN HILL UNIVERSITY
SHILLONG 793022

Applications with complete bio-data from candidates possessing the required qualifications are invited for the posts of JRF (1) and Project Assistant (1) in DBT, GOI-funded research project “Next Generation Sequencing (NGS)- based de novo assembly of expressed transcripts and genome information of Orchids in North-East India” in DBT’s Twinning programme for NE as per DBT sanction order and norms.

(i) JRF(1 no.):

Qualifications: M.Tech/M.Sc in Life Sciences/ Botany/ Zoology/ Biochemistry/ Biotechnology/ Bioinformatics;

Desirable: Aptitude for Bioinformatics and Computer Programming/ Next generation sequencing data analysis

(ii) Project Assistant (1 no.):

Qualifications: Graduation in Science,

Desirable: Experience of working in a Life Science/Plant Biotechnology lab. and familiarity with computers and field work viz. collection of samples.

The applications through email bicnehu@gmail.com or post must reach the undersigned within 15 days from the date of publication of this advertisement. The advertised posts are purely temporary for the duration of the project and subject to availability of the funds from DBT. The appointment does not confer any entitlement or right over the posts for absorption in the University service. Prof. Pramod Tandon, PI/Mr. Devendra Kumar Biswal (Co-PI) email: bicnehu@gmail.com

Advertisement: www.nehu.ac.in/Advertisements/BIC_AdvtPV_030815.pdf

Cancer research database

Neel — Tue, 01 Sep 2015 17:36:31 -0500

Researchers in Andhra Pradesh have developed a database to identify genes that are common in tumours to provide their colleagues with easy access to insights into the genetic alterations in cancer.

The database, hosted at the Sri Venkateswara University (SVU) in Tirupati, will integrate information on cancer genes and markers with experimental data.

The Cancer Gene Markers Database (CGMD) is meant to help scientists better understand tumour genes and markers at a molecular level by combining data with literature on treatment regimen and recent advances in cancer therapy.

The database is free to access, and already includes 309 genes and 206 markers that correspond to 40 different human cancers. Accompanying literature comes from databases such as the United States’ National Center for Biotechnology Information and the Kyoto Encyclopedia of Genes and Genomes. It also includes experimental data from PubMed.

In a paper published last month in Nature Scientific Reports, the researchers from SVU’s department of animal biotechnology, describes the need for a database for different genes and markers along with their molecular characteristics and pathway associations.

Guest Faculty Job vacancies in Pondicherry University

Tue, 22 Sep 2015 23:50:16 -0500

Guest Faculty Job vacancies in Pondicherry University
Qualification : M.Phil. / M.Tech. / M.Sc. in Computer Science / Master of Computer Applications with a minimum of 55% of marks. Candidates with Ph.D. degree and NET/SLET qualification will be given preference as per UGC norms.

Desirable : Research or teaching experience in Bioinformatics and Computational Biology.
Honorarium : Rs. 1,000/- per lecture (subject to a maximum of 25,000/- per month)
How to apply

Interested eligible candidates may attend the 'walk-in' interview along with all original certificates and testimonials with a copy of their bio-data. Walk-in-interview will be held on 28.09.2015 (Monday), 03:00 P.M. at the office of the Dean, School of Life Sciences, Science Block — I, Pondicherry University, Puducherry — 605 014. Candidates reporting after 03:00 P.M. will not be entertained.

More at http://www.pondiuni.edu.in/news/walk-interview-guest-faculty-centre-bioinformatics

Postdoctoral positions are available at the Faryabi Lab

Sun, 11 Oct 2015 03:36:18 -0500

Postdoctoral positions are available at the Faryabi Lab located in the Department of Pathology and the Center for Personalized Diagnostics at the University of Pennsylvania.

A qualified candidate will be strongly motivated individual with following qualifications: a Ph.D. in computational sciences, engineering, physics, bioinformatics, or related field. Ability to program in Python/Perl and R in Unix environment, knowledge of C++, Java, and SQL is a plus. Demonstrated applied bioinformatics/computational proficiency as evidenced by relevant publications in peer-reviewed journals. Experience with cancer genomics is a plus.

The primary research focus of the Faryabi Lab is on developing novel computational methods to study mechanisms involved in genome instability and elucidate their roles in tumorigenesis. In addition the position provides collaborative opportunities with both basic and translational scientists across the Perelman School of Medicine, one of the top 5 medical research universities in the nation.
. a Ph.D. degree in either physical or computational sciences
. solid programming skills ( Python/Perl, Java, C/C++, R, SQL)
. computational genomics experience ( high throughput sequence analysis)
. excellent spoken and written communication and interaction skills
. publications in English in relevant areas of research in peer-reviewed journals.
. Previous experience or interest in data visualization design is a plus.

More at
University of Pennsylvania
Pathology and Laboratory Medicine
Robert B. Faryabi
faryabiPenn@gmail.com
http://faryabib.github.io/
How To Apply: email CV and contacts of 3 references to faryabiPenn@gmail.com

Kamaleshwar Singh Lab

Fri, 25 Mar 2016 10:46:49 -0500

The focus of Dr. Singh’s research and teaching is on the molecular mechanistic basis for environmental carcinogen-induced genetic (DNA damage) and epigenetic changes, and susceptibility to human cancer development

More at http://www.tiehh.ttu.edu/dr.-kamaleshwar-singh.html

ASSISTANT PROFESSOR Bioinformatics at ALAGAPPA UNIVERSITY

Thu, 03 Dec 2015 23:30:43 -0600

ALAGAPPA UNIVERSITY
Recruitment and Sarkari Naukri for the Post of ASSISTANT PROFESSOR Bioinformatics
Job Description UGC scale of pay is applicable. For eligibility qualifications and other norms, please refer to the ?Instructions to the Candidates? available with the application forms which can be had on payment of Rs.520/- inclusive of Rs.20/- for postage. For SC/ST, Rs.320/- inclusive of Rs.20/- for postage on enclosure of a copy of the community certificate. Payment is to be made by means of Demand Draft drawn on any nationalized bank in favour of ?The Registrar, Alagappa University? payable at Karaikudi. Candidates can also download the application form and instructions to the candidates from httpwww.alagappauniversity.ac Filled-in application should reach on or before 19.10.2015
Salary for Job : Rs.15600-39100+AGP Rs.6000
Education : Good academic record with at least 55 marks (or an equivalent grade in a point scale wherever grading system is followed) at the Masters Degree level in a relevant subject from an Indian University, or an equivalent degree from an accredited foreign university. Besides fulfilling the above qualifications, the candidate must have cleared the National Eligibility Test (NET) conducted by the UGC, CSIR or similar test accredited by the UGC like SLET/SET.Notwithstanding anything contained in sub-clauses (i) and (ii) above, the candidates, who are, or have been awarded a Ph.D. degree in accordance with the University Grants Commission (Minimum Standards and Procedure for Award of Ph.D. Degree) Regulations 2009, shall be exempted from the requirement of the minimum eligibility condition of NET/SLET/SET for recruitment and appointment of Assistant Professor or equivalent positions in Universities/Colleges/Institutions.
Number of Vacancies : 02
Naukri Location : Other City(s) in Tamil Nadu
Address : KARAIKUDI ? 630 003
Last Date to Apply : 2015-12-04
Apply Process : written test/interview

Chekulaevalab

Tue, 12 Jan 2016 02:32:03 -0600

Focusing on understanding the molecular mechanisms that regulate mRNA translation, localization and stability and role of non-coding RNAs in this process. Up to 90% of human DNA is estimated to be transcribed into so called non-coding RNAs that are not translated into proteins. Many of them act as potent modifiers of gene expression. miRNAs are a class of such short non-coding RNAs. They regulate expression of more than a half of eukaryotic genes, thus, affecting multiple biological processes, including cell proliferation, differentiation, apoptosis and senescence. Not surprisingly, miRNAs are involved in many human pathologies, including cancer and neurological disorders and hold great potential as drug targets, disease markers, as well as therapeutic agents.
Our lab is located at the Berlin Institute for Medical Systems Biology (BIMSB), a part of the Max Delbrück Center for Molecular Medicine (MDC).

http://www.chekulaevalab.org/

MAKER

Jitendra Narayan — Sun, 07 Feb 2016 15:59:24 -0600

MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values.

More at http://www.yandell-lab.org/software/maker.html

Address of the bookmark: http://www.yandell-lab.org/software/maker.html