BOL: Related items

bacLIFE: an automated genome mining tool for identification of lifestyle associated genes

BioStar — Fri, 15 Mar 2024 04:59:14 -0500

bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and biosynthetic gene clusters associated with each lifestyle detected. This whole process is divided into different modules:

Clustering module Predicts, clusters and annotates the genes of every input genome
Lifestyle prediction Employs a machine learning model to forecast bacterial lifestyle or other specified metadata
Analitical module (Shiny app) Results from the previous modules are embedded in a user-friendly interface for comprehensive and interactive comparative genomics.

You can find the complete wiki here [https://github.com/Carrion-lab/bacLIFE/wiki/bacLIFE-wiki]

Address of the bookmark: https://github.com/Carrion-lab/bacLIFE

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...

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

Shruti Paniwala — Fri, 03 Jan 2020 13:28:19 -0600

DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life.

Address of the bookmark: https://github.com/YoannAnselmetti/DeCoSTAR_pipeline

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.

Protein Subcellular Localization Prediction

Poonam Mahapatra — Thu, 01 Mar 2018 06:20:47 -0600

Assigning subcellular localization to a protein is an important step towards elucidating its interaction partners, function, and potential role(s) in the cellular machinery. Computational tools offer an attractive complement to time-consuming and laborious experimental methods.

http://abi.inf.uni-tuebingen.de/Services/YLoc/webloc.cgi

Address of the bookmark: https://abi.inf.uni-tuebingen.de/Research/Systems%20Biology/protein-subcellular-localization

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

RNAcon: web-server for the prediction and classification of non-coding RNAs

Shruti Paniwala — Mon, 17 Jul 2017 04:55:11 -0500

RNAcon is a web-server for the prediction and classification of non-coding RNAs. It uses SVM-based model for the discrimination between coding and ncRNAs and RandomForest-based prediction model for the classification of ncRNAs into different classes. The structural information based graph properties were used for the development of prediction model.

The standalone version (Linux-based command-line) of RNAcon is freely available for the global scientific community.

Reference: Panwar, B.; Arora, A. and Raghava, G.P.S. (2014) Prediction and classification of ncRNAs using structural informationBMC Genomics 2014, 15:127

Address of the bookmark: http://crdd.osdd.net/raghava/rnacon/

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

STRUM: structure-based prediction of protein stability changes upon single-point mutation

BioStar — Mon, 10 Sep 2018 13:21:49 -0500

STRUM is a method for predicting the fold stability change (ΔΔG) of protein molecules upon single-point nsSNP mutations. STRUM adopts a gradient boosting regression approch to train the Gibbs free-energy changes on a variety of features at different levels of sequence and structure properties. The unique characteristics of STRUM is the combination of sequence profiles with low-resolution structure models from protein structure prediction, which helps enhance the robustness and accuracy of the method and make it applicable to various protein seqences, including those without experimental structures

Address of the bookmark: https://zhanglab.ccmb.med.umich.edu/STRUM/

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