BOL: Related items

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

The Day We Began Reading the DNA of the World

Jitendra Narayan — Sat, 05 Sep 2026 01:43:21 -0500

Picture waking up and knowing that in one lab, a scientist is reading the DNA of a whale. In another, a team is sequencing a rare plant. Meanwhile, researchers in India are decoding the genomes of different human populations.

Many organisms. Many countries. All share one remarkable goal: to understand the genetic story of life.

DNA is nature's instruction manual, written with just four letters: A, T, C, and G. For years, scientists could only read small sections of this huge book. Now, new sequencing technology lets us read entire genomes like never before.

One of the most ambitious projects is the Earth BioGenome Project (EBP). Its goal is to create reference genomes for about 1.5 million known eukaryotic species. This project links genome research across continents, species, and scientific fields.

But this story goes beyond just animals and plants.

A New Chapter in Human Genomics

Large human genome projects are changing how we understand our own genetic diversity.

India's GenomeIndia project has sequenced thousands of people from different populations. This work is uncovering genetic variation that global databases have often missed.

Similar population-scale effSimilar large-scale projects are happening worldwide. The All of Us Research Program in the United States, Europe's 1+ Million Genomes initiative, South Korea's national genomic data program, and projects in Saudi Arabia, Australia, and Singapore are all building huge genomic resources.collect DNA.

The real goal is to link genomes with health, disease, and other biological information. This creates a base for more accurate research and, in time, more personalized medicine.

A Race Against Time

There is also an important twist.

We are sequencing Earth's biodiversity even as many species face growing environmental threats.

A genome alone cannot save a species, but it does keep important information about its biology, evolution, and genetic diversity. This knowledge helps scientists understand risks, guide conservation, and find traits that could help agriculture or medicine.

Projects like the Darwin Tree of Life, which studies species in Britain and Ireland, and the African BioGenome Project, which is growing genomics work across Africa, are key parts of this worldwide effort.

Projects to Watch

Earth BioGenome Project (EBP) - A global effort to sequence and annotate roughly 1.5 million known eukaryotic species and create a comprehensive reference library of Earth's biodiversity.
Vertebrate Genomes Project (VGP) - Focuses on producing high-quality reference genomes for vertebrate species, providing a major foundation for the wider Tree of Life.
Darwin Tree of Life - A UK and Ireland initiative aiming to sequence approximately 70,000 species, creating a detailed genomic map of regional biodiversity.
African BioGenome Project (AfricaBP) - A pan-African initiative focused on sequencing Africa's biodiversity while strengthening genomics and bioinformatics capacity across the continent.
European Reference Genome Atlas (ERGA) - A European effort to generate high-quality reference genomes for Europe's biodiversity and connect national sequencing efforts.
Canada BioGenome Project - Building reference genomes for Canadian biodiversity, supporting conservation, research and the study of ecosystems.
California Conservation Genomics Project - Uses genomics to understand and protect California's biodiversity and help inform conservation decisions.
Bat1K - An ambitious global effort to sequence the genomes of all known bat species, helping scientists study their evolution, longevity, immunity and unique biology.
Bird 10,000 (B10K) - A global project aiming to create genome resources covering the world's bird diversity and reconstruct avian evolutionary history.
Global Invertebrate Genomics Alliance (GIGA) - Builds genomic resources for the enormous and genetically diverse world of invertebrates.
GenomeIndia - India's national human-genome initiative, designed to capture the country's extraordinary population diversity and create a reference resource for Indian genomics.
All of Us Research Program - A US national research program combining genomic information with health and lifestyle data at population scale.
1+ Million Genomes / Genome of Europe - A European effort to enable secure, cross-border use of genomic and health data and develop genome-scale resources involving more than one million people.
Korea National Integrated Bio Big Data Project - South Korea's large-scale national effort combining genomic and health information from a very large population cohort.
Saudi Genome Program - A national genomics initiative focused on genetic diseases, population genomics and precision medicine in Saudi Arabia.
Australian Genomics / Genomics Health Futures Mission - Australia's growing investment in genomic medicine, rare disease research and population-scale health genomics.

The Library of Life

The fuThe future of genomics is not just about sequencing one genome at a time. Now, it is about creating a worldwide network of genomes—human and non-human, individual and species—linked by powerful databases and advanced computational tools.ine a library without shelves.

In this library, the books are genomes. The pages are made of DNA. Scientists and machines are the readers. And this library is still being written. Each genome sequenced today adds a new page to the story of life and helps us better understand our place in it.

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...

Claus-Peter Stelzer Lab

Mon, 15 Mar 2021 15:24:41 -0500

Interested in various topics at the intersection of ecology and evolution. In my research I use rotifers as model organisms for experimental studies at the individual and population level. Rotifers are ideally suited for this, because populations of thousands can be kept in small containers in the lab, while single individuals can still be handled conveniently.

More at https://www.uibk.ac.at/limno/personnel/stelzer/index.html.en#research

TEDMED Great Challenges: Genomics and Medicine: Where promise meets clinical practice

Fri, 22 Nov 2013 12:05:32 -0600

November 21, 2013 - NHGRI Director Eric Green, M.D., Ph.D, hosted the TEDMED Google+ Hangout to discuss genomic medicine with an all-star cast that includes Carlos Bustamante, James Evans, Amy McGuire and Sharon Terry. More: http://www.tedmed.com/greatchallenges

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

MedGenome is looking for Genome Analysts

Fri, 01 Jan 2021 11:06:23 -0600

MedGenome is looking for Genome Analysts (5-6 Positions), ambitious and energetic who will work both independently and as part of a collaborative team to generate data from various genomics-oriented workflows and assist in the optimization and validation of new technologies and procedures.
• Master’s in Science, 0 – 4 years of relevant experience
• Interpretation of variants/mutations causing genetic disorders using standard guidelines.
• Support in data analysis of projects

Reach out to careers@medgenome.com with your detailed profile.

Faculty post at Zhejiang University

Tue, 10 Jun 2014 03:40:40 -0500

Zhejiang University (ZJU) is seeking faculty candidates for its newly launched, highly competitive and well funded “Hundred Talents Program”. This search covers all colleges and departments at ZJU. Applicants, expected to be about 35 years old, should hold PhD degree, and postdoctoral experiences are preferred for applicants in most fields. Applicants should have demonstrated commitment to excellence in teaching and research at a level comparable to the academic achievement of assistant professor or associate professor in world-renowned universities. Successful candidates must work full-time and are expected to establish internationally competitive and independent research program in cutting-edge areas of the relevant field at ZJU.

As one of the leading research-intensive universities in China, ZJU is located in the beautiful city of Hangzhou. Successful candidates will be employed as Principal Investigators and are qualified to supervise doctoral students. ZJU will offer an internationally competitive salary and the opportunity to purchase university's apartment at a price much lower than the market price, and will provide office and laboratory spaces as well as internationally competitive research startup packages.

Qualified applicants are strongly encouraged to submit their applications electronically to tr@zju.edu.cn. Applicants should include the following materials in pdf format: a comprehensive CV, a statement of research and teaching plan, and a list of 3 to 5 references with detailed contact information.

Contact：Talents Office, ZJU

Tel：+86-571-88981345, +86-571-88981390

Fax：+86-571-88981976

E-mail:tr@zju.edu.cn

Scripted DNA !!!

Jit — Mon, 17 Aug 2015 17:44:04 -0500

As per bioinformatician DNA is partially scripted ;) You dont believe in it. Please have a look at image carefully:)

XAMPP: Starting Apache fail Ubuntu

Ram Yash Pal — Sat, 07 Jun 2014 05:52:35 -0500

Once you install XAMMP on linux, the most common problem you face is Apache failure. To fix the issues please use following command to first stop and then again start it.

sudo /etc/init.d/apache2 stop

sudo /etc/init.d/mysql stop

sudo /etc/init.d/proftpd stop

sudo /opt/lampp/lampp start

PhpMyAdmin “Wrong permissions on configuration file, should not be world writable!”

Once the Xammp is installed, it might be possible to set up the configuration file in writable mode. Try the following steps:

Just chmod 0755 the file

sudo chmod 0755 config.inc.php