BOL: Related items

RA at IISR Kozhikode

Thu, 15 May 2014 10:08:09 -0500

INDIAN INSTITUTE OF SPICES RESEARCH
(Indian Council of Agricultural Research)
Marikunnu P.O., Kozhikode – 673 012, Kerala

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

Python Education Material

Jitendra Narayan — Wed, 10 Jul 2013 16:38:23 -0500

Google provide free class for people with a little bit of programming experience who want to learn Python. The google python class includes written materials, lecture videos, and lots of code exercises to practice Python coding. These materials are used within Google to introduce Python to people who have just a little programming experience.

Find more @ https://developers.google.com/edu/python/

Professor/Associate Professor/ Assistant Professor at Chettinad Academy of Research and Education

Sat, 24 May 2014 00:00:15 -0500

OPEN FACULTY POSITION

Chettinad Academy of Research and Education (CARE) invites applications from eligible and translational research-oriented candidates to the posts of Professor/Associate Professor/ Assistant Professor Computational Biology, Bioinformatics, and Pharmaceutical Chemistry.

Emoluments: As per UGC norms (Adequate Compensation for Postdoctoral/Teaching experience)

Candidates fulfilling the eligibility criteria as per the UGC norms can send their full CV with copies of certificates and reference letters to the following address by post or by e-mail on or before 31st May 2014

The Registrar,
Chettinad Academy of Research and Education,
Chettinad Health City
Kelambakkam, Chennai 603 103
Tamil Nadu
T +91 (0)44 4741 1000
F +91 (0)44 4741 1011
Email: jobs @chettinadhealthcity.com

Advertisement: http://182.73.176.163/chc/ads2014.pdf

The Minerva Research Group for Bioinformatics

Tue, 27 May 2014 15:48:14 -0500

The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.

http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27

Kelso Group
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
Germany
Phone: +49 341 3550 500

Job:
http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40

Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees

Rahul Nayak — Wed, 27 Nov 2019 05:32:33 -0600

The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported).

Other tools

https://github.com/shenwei356/taxonkit

ETE, version: 3.1.1
BioPython, version: 1.73
taxadb, version: 0.10.1
TaxonKit, version: 0.5.0

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/

Monitor running jobs on Linux server

Jitendra Narayan — Fri, 06 Jun 2014 16:18:43 -0500

You as a bioinformatican run lots of program on your servers. Sometime the shared server is also used by your colleague. If server is busy you sometime need to check the running programs and want to monitor the running programs as well. The "top" command will come in handy when you need to find out if things are still running, how long they’ve been running, or how much memory is being used.

‘top’ is very simple to run: type

%% top

You’ll get a screen that looks like this, and is updated regularly:

Simple, right? Heh.

First! Note that you can use ‘q’ or ‘CTRL-C’ to exit from ‘top’.

Now let’s read and understand at each line independently.

The first line:

top - 23:00:48 up 39 days, 2 user, load average: 0.00, 0.00, 0.00

The first line tells you the current time, how long the machine has been up, how many users are logged in, and the short/medium/long-term compute load on the machine. If you run something for a long time, you’ll see these numbers go up. Right now, the machine is basically just sitting there, so these are all close to 0.

The second line:

Tasks: 239 total,   1 running, 238 sleeping,   0 stopped,   0 zombie

This line tells you how many processes are running. If you are using laptops machines it’s not so interesting because you really are the only one using this machine.

Cpu(s): 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st

This line contains the CPU load. The first two numbers are how busy the system is doing computation (“us” stands for “user”) and how busy the system is doing system-y things like accessing disks or network (“sy” stands for “system”). We’ll talk more about this later.

Mem:   49457320k total,    3492174k used, 14535596k free,    1435148k buffers

This should be easy to understand – how much memory you’re using!

Swap:   539356k total,   28332k used,   836562k free,    29862014k cached

Swap is just on-disk memory that can be used to “swap” out programs from main memory. Again, we’ll talk about this later.:

PID USER      PR NI VIRT RES SHR S %CPU %MEM    TIME+ COMMAND
1 root      39 19 0 0 0 S 0.0 0.0   246:57.22 kipmi0
2 root      RT   0     0    0    0 S 0.0 0.0   0:00.00 migration/0

And... finally! What’s actually running! The two most important numbers are the %CPU and %MEM towards the right, as well as the COMMAND. This tells you how compute- and memory-intensive your program is. Right now, nothing’s running so the numbers aren’t very interesting, but just wait until we run something...

Flanker

Rahul Nayak — Sat, 27 Feb 2021 22:04:53 -0600

Flanker, a Python package which performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of mobile genetic elements (MGEs) without prior knowledge of their structure. Flanker can be flexibly parameterised to finetune outputs by characterising upstream and downstream regions separately and investigating variable lengths of flanking sequence.

Address of the bookmark: https://github.com/wtmatlock/flanker

Genomics and Personalized Medicine Breakthroughs

Sun, 01 Jun 2014 23:40:14 -0500

http://bit.ly/e8QGzY Human genome mapping is now enabling a breakthrough in medical innovation -- personalized medicine. What does this mean for patients? We can now identify predispositions to disease, predict how we metabolize drugs, and figure out what kinds of treatments we may respond to, and even determine when a drug may give us an adverse reaction. All medical specialties benefit from human genome intelligence -- oncology saw the first impacts -- but advances are now being seen in cardiology, obstetrics and gynecology, pediatric diseases, gastroenterology, rheumatology, immunology and other areas. This video covers the areas that genetic medicine is impacting and where the future of genomic medicine is heading.

jobTree based python wrapper to run the genome simulation tool suite Evolver

Jit — Fri, 08 Dec 2017 16:26:32 -0600

evolverSimControl (eSC) can be used to simulate multi-chromosome genome evolution on an arbitrary phylogeny (Newick format). In addition to simply running evolver, eSC also automatically creates statistical summaries of the simulation as it runs including text and image files. Also included are convenience scripts to: check on a running simulation and see detailed status and logging information; extract fasta sequence files from the leaf nodes of a completed simulation; extract pairwise multiple alignment files (.maf) from leaf and branch nodes from a completed simulation and with the help of mafJoin, join them together into a single maf covering the entire simulation.

Address of the bookmark: https://github.com/dentearl/evolverSimControl

Assistant Professor in Bioinformatics at Dr. D. Y. Patil Biotechnology & Bioinformatics Institute

Tue, 03 Jun 2014 19:54:15 -0500

Dr. D. Y. Patil Biotechnology & Bioinformatics Institute
Tathawade, Pune 411033.

Assistant Professor in Bioinformatics

Essential :
First Class Master’s Degree in the appropriate branch of Life Sciences / Technology (Tech.)
OR
Ph.D in Life Sciences or in the respective subject area of specialization
OR
Good Academic record with at least 55% marks (or an equivalent grade) at the Master’s Degree level, in the relevant subject or an equivalent degree from an Indian / Foreign University.
Besides fulfilling the above qualifications, candidates should have cleared the eligibility test (NET) for lecturers conducted by the UGC, CSIR or similar test accredited by the UGC and as per the requirements of UGC guidelines.

Desirable :
Teaching, research industrial and/or professional experience in a reputed organization.
Papers presented at Conferences and/or in refereed journals

Note : Application are invited in prescribed form Click here for Application Form
Kindly send your applications to “Registrar, Dr. D. Y. Patil Vidyapeeth, Pune, Sant Tukaram Nagar, Pimpri, Pune – 411018., Maharashtra, India.” should reach in the University office within 15 days from the publication.

More Info: http://www.dpu.edu.in/BiotechResearchPositions.aspx