<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/7913?offset=1270 https://bioinformaticsonline.com/pages/view/11582/monitor-running-jobs-on-linux-server Fri, 06 Jun 2014 16:18:43 -0500 https://bioinformaticsonline.com/pages/view/11582/monitor-running-jobs-on-linux-server <![CDATA[Monitor running jobs on Linux server]]> 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:

image
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...

]]> Jitendra Narayan https://bioinformaticsonline.com/bookmarks/view/42985/janggu-deep-learning-for-genomics Tue, 23 Mar 2021 05:14:43 -0500 https://bioinformaticsonline.com/bookmarks/view/42985/janggu-deep-learning-for-genomics <![CDATA[Janggu - Deep learning for Genomics]]> Janggu is a python package that facilitates deep learning in the context of genomics. The package is freely available under a GPL-3.0 license.

Detail tutorial at https://janggu.readthedocs.io/en/latest/

USE cases

https://github.com/wkopp/janggu_usecases

Address of the bookmark: https://github.com/BIMSBbioinfo/janggu

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34515/metasim-a-sequencing-simulator-for-genomics-and-metagenomics Mon, 04 Dec 2017 07:18:20 -0600 https://bioinformaticsonline.com/bookmarks/view/34515/metasim-a-sequencing-simulator-for-genomics-and-metagenomics <![CDATA[MetaSim A Sequencing Simulator for Genomics and Metagenomics.]]> Our software can be used to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets. Based on a database of given genomes, the program allows the user to design a metagenome by specifying the number of genomes present at different levels of the NCBI taxonomy, and then to collect reads from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a given evolutionary tree. 

Address of the bookmark: http://ab.inf.uni-tuebingen.de/software/metasim/

]]> Jit https://bioinformaticsonline.com/opportunity/view/36647/bioinformatics-jobs-at-nibmg Wed, 16 May 2018 02:57:15 -0500 <![CDATA[Bioinformatics jobs at NIBMG]]> NIBMG are looking for bright and motivated people in our big projects on cutting edge biomedical genomics research

http://www.nibmg.ac.in/academic/SyMeC-ICGC/SyMeC%20&%20ICGC_May%202018.pdf

http://www.nibmg.ac.in/academic/plp/15_05_2018/AdvertisementMay2018.pdf

]]> https://bioinformaticsonline.com/opportunity/view/11656/faculty-post-at-zhejiang-university Tue, 10 Jun 2014 03:40:40 -0500 <![CDATA[Faculty post at Zhejiang University]]> 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

]]> https://bioinformaticsonline.com/blog/view/11592/xampp-starting-apache-fail-ubuntu Sat, 07 Jun 2014 05:52:35 -0500 https://bioinformaticsonline.com/blog/view/11592/xampp-starting-apache-fail-ubuntu <![CDATA[XAMPP: Starting Apache fail Ubuntu]]> 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
]]> Ram Yash Pal https://bioinformaticsonline.com/researchlabs/view/42137/plant-computational-genomics-lab-%E2%80%93-jill-wegrzyn Thu, 20 Aug 2020 19:49:12 -0500 <![CDATA[PLANT COMPUTATIONAL GENOMICS LAB – JILL WEGRZYN]]> Our research focuses on the computational analysis of genomic and transcriptomic sequences from non-model plant species. We do this by developing approaches to examine gene finding, gene expression, transcriptome assembly, and conserved element identification, through machine learning and computational statistics. We use these novel methods to address questions related to genome biology and population genomics.

We also develop web-based applications that integrate data across domains to facilitate the forest geneticist or ecologist’s ability to analyze, share, and visualize their data. Such integration requires the implementation of semantic technologies and ontologies to connect genotype, phenotype, and environmental data.

http://plantcompgenomics.com/

]]> https://bioinformaticsonline.com/opportunity/view/42712/scientist-c-non-medical-it-expert-computer-professionalgenomicsbioinformatic-at-nimr Mon, 01 Feb 2021 13:54:06 -0600 <![CDATA[Scientist C - Non-Medical (IT Expert- Computer Professional/Genomics/Bioinformatic) at NIMR]]> Applications are invited upto 12th February 2021 in the prescribed format (available on the websites of ICMR-NIMR) through link http://onlineapply.nimr.org.in/ up to 05:00 PM on 12th February 2021 for the following post on contract basis at NIMR, Sector-8, Dwarka, New Delhi.

Scientist C - Non-Medical (IT Expert- Computer Professional/Genomics/Bioinformatic)No. of posts: 01 (UR)

Salary (Fixed): Rs.51,000/- + HRA

Essential Qualification: Candidate should possess 1st class master degree in relevant subjects from a recognized university with 4 years experience
OR
2nd class M.Sc + Ph.D degree in relevant subjects from a recognized university with 4 years experience.Desirable Qualification: Candidates should possess a PhD degree in any field of science.
Preference will be given to those who have published scientific papers in international journals and who have a track record of working in infectious diseases.

The candidate must know the following for further consideration: (a) data processing and analysis using statistical softwares, (d) programming, (e) presentation of complex data from excel files and related skills.
Understanding of GIS and malaria will be an advantage. Experience and interest in functional genomics and genomic sequencing will be important.

Age Limit: 40 YearsDuration: 30.09.2021

More at http://onlineapply.nimr.org.in/

]]> https://bioinformaticsonline.com/opportunity/view/12594/faculty-positions-at-central-university-of-punjab Mon, 07 Jul 2014 23:33:33 -0500 <![CDATA[Faculty Positions at Central University of Punjab]]> Faculty Positions: Rolling/Open Advertisement Advt.No: T-10 (2013)

Pay Scale: Pay Band Rs.15600-39100 with AGP of Rs.6,000/-

Essential Qualifications for Professors, Associate Professors, and Assistant Professors: As per “UGC REGULATIONS ON MINIMUM QUALIFICATIONS FOR APPOINTMENT OF TEACHERS AND OTHER ACADEMIC STAFF IN UNIVERSITIES AND COLLEGES AND MEASURES FOR THE MAINTENANCE OF STANDARDS IN HIGHER EDUCATION 2010“ and the 2nd Amendments to the regulation issued in June 2013.

For details: http://www.ugc.ac.in/oldpdf/regulations/revised_finalugcregulationfinal10.pdf http://www.ugc.ac.in/pdfnews/8539300_English.pdf and University rules.

Procedure to apply:

Application forms along with API form complete in all respect along with necessary documents and application fee of Rs. 500/-. (Rs. 250/- for Scheduled Caste/Scheduled Tribe/Person with disabilities) should be sent to:

Registrar, Central University of Punjab, City Campus, Mansa Road, Bathinda-151001

For more info visit: http://www.centralunipunjab.com/Teaching/Final%20Details-t10-2013.pdf, http://www.centralunipunjab.com/Teaching/Advertisement-t10-2013.jpg

Last Apply Date: 31 Dec 2014

]]> https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources Tue, 28 Jun 2022 04:08:06 -0500 https://bioinformaticsonline.com/blog/view/43896/list-of-comparative-genomics-resources <![CDATA[List of comparative genomics resources !]]>

Compare structural and functional annotations of proteins between sequenced genomes.

View AREs in the human transcriptome and study the comparative genomics of AREs in model organisms.

Find information about orthologous genes in prokaryotes.

Search for publicly available QTL data on livestocks and animal species.

Find information about bovine genomics data.

A multi-organism web-based resource system designed to easily retrieve, correlate and interpret data across species.

A database resource of developmentally associated conserved non-coding elements.

Delineate conserved non-coding blocks from upstream regions of putative orthologous gene pairs from man, mouse, rat, fugu, Mus musculus, Danio rerio, and zebrafish.

Find coexpressed gene lists and networks in human and mouse.

Construct phylogenetic tree of microorganisms based on oligopeptide content of their complete proteomes.

A novel database server that classifies GenBank's dbEST (database of expressed gene sequences) libraries and removes contaminants.

Find information about the ancestral relationship between genes.

Provides an overview of the genomic organization of microRNAs and extent of conservation during evolution in different metazoan species.

Conduct comparative biometric analysis of chromosomes of different organisms.

Search for Indices of gene and transcripts in human and mouse.

Search and compare 12 new and old Drosophila genomes.

Access to whole genome alignments of human, mouse, rat and fish sequences.

Find eukaryotic paralog/paralogon information.

Analyze the evolutionary process of overlapping genes when comparing different species.

The first publicly available system reported to handle inter-species gene mention normalization.

A web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes.

Visualize gene indices of human, mouse, Arabidopsis, Zebrafish, Drosophila and Sheep.

Find information about mutated mouse genes.

A data management and analysis system for metagenomes

Search for influenza sequence, vaccine, and drug resistance information.

LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal models for their research.

The missing link between multi-species full genome comparisons and functional analysis.

Conduct comparative analysis of completely sequenced microbial genomes.

A biologist-centric software for evolutionary analysis of DNA and protein sequences.

Conduct single nucleotide polymorphisms diversity measurements among homologous sequences from the Mammalia class.

Find information about 1000s of microbial genomes.

A database dedicated to the study of genome conservation.

Explore orthologous relations across 352 complete genomes.

Browse complete genomes in several clades.

A database of orthologous genomic markers for placental mammal phylogenetics.

Conduct genome wide functional and structural analysis.

Conduct genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes.

Compare phenotypes of a given gene or gene set in different model organisms.

Phylemon is a web server that integrates a selected suite of more than 20 different tools from the most popular stand-alone programs of phylogenetic and evolutionary analysis.

Use this database to see where in the evolution some phylogenetic lineages were started, and over which species they were contained.

Search for genomic information on nematode satellite species Pristionchus pacificus.

Find information about related protein sequences.

Database hosting genomics and post-genomics data from multiple protozoans.

A database of pseudogene families based on the protein families from the Pfam database.

Find genomic information about mammals.

Find information about predicted regulons in prokaryotic transcription regulation.

Perform systematic comparison of proteome data among species.

A comparative map viewer dedicated to the biology of the Solanaceae family.

Analyze data from functional analysis on fragmented microbial genetic material.

Visualize and explore comparative genomic hybridization data sets.

Search for genome-wide annotations of regulatory sites in yeast and prokaryotes genomes.

Search for information on adaptive evolution in gene families of higher plants and chordate.

Generate graphical maps of circular genomes that show sequence features, base composition plots, analysis results and sequence similarity plots.

Conduct a comprehensive analysis of genes and genomes.

An interactive online poster presentation on the Macaque genome, including high-quality images, video clips, and Web resources

Search for annotated genetic information of expressed sequence tags (ESTs) in different eukaryotic organisms.

Find mapping and expression information for a unigene cluster (ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene)

A public online resource for identifying or designing 'universal' overgo-hybridization probes from conserved sequences that can be used to efficiently screen one or more genomic libraries from a designated group of species.

Comprehensive suite of programs and databases for comparative analysis of genomic sequences.

Find metabolic networks and phylogenomic information on a taxonomically diverse range of eukaryotes.

]]> Shruti Paniwala