BOL: Related items

JPred4: A Protein Secondary Structure Prediction Server

Poonam Mahapatra — Fri, 29 Dec 2017 16:14:28 -0600

JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction.

Address of the bookmark: http://www.compbio.dundee.ac.uk/jpred4/

Bioinformatics JRF/SRF position at NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY

Sun, 11 May 2014 22:29:12 -0500

NATIONAL RESEARCH CENTRE ON PLANT BIOTECHNOLOGY
LBS, CENTRE, PUSA CAMPUS, IARI NEW DELHI
NEW DELHI – 110 012

WALK- IN –INTERVIEWS

Eligible candidates may appear in Walk-in-Interview on May 23, 2014 at 10 AM for the posts of Research Associates & Senior Research Fellows (SRF) in the following DST/DBT/ICAR funded projects.

1 NPTC Project on Bioinformatics and Comparative Genomics

Research Associate (One)

Rs. 24000/- + 30% HRA for masters degree holder with more than 4 years experience

Essential: Ph D in Plant Molecular Biology & Biotechnology/Genetics 0r Candidates who have already submitted their Ph D thesis in above subjects

Desirable: Research experience in Genomics, Molecular biology, Microarrays analysis, Gene cloning, transgenic Techniques , and computational analysis.

Senior Research Fellow ( UGCCSIR/ DBT/ ICAR Net qualified only): (One)

Rs. 16000/- + 30% HRA and Rs. 18000+30 HRA from 3rd year onwards

Essential:

1. ICAR/ UGCCSIR/DBT Net qualified only

2. M. Sc. (with thesis) in Biotechnology, Life Sciences, Biosciences/ Bioinformatics, Genetics/ Plant Pathology with experience in molecular biology.

Or M.Sc with more than 3 years research experiences

3. B.Sc. Agriculture or Biology

Desirable:
1. M. Sc. with thesis
2. Experience in molecular biology, plant tissue culture
3. Bioinformatics knowledge is important

2 DST JC Bose National Fellowship

Research Associate (Bioinformatics) : One

Rs.22000/- + 30% HRA for 1 & 2nd Yr., Rs. 23000+ 30% HRA for 3rd year and Rs. 24000+30% HRA for 4th &5th yr

Essential: M Ph D in Plant Molecular Biology & Biotechnology/Genetics

Desirable: Research experience in Genomics, Molecular biology, Microarrays analysis, Gene cloning, transgenic Techniques , and computational analysis.

Age limit: Max.35 years (Age relaxation of 5 years for SC/ST & women and 3 years for OBC)

The posts are purely temporary in nature and are co-terminus with the project. Initially the offer will be made for one year only and may be further extendable based on performance of the candidate. The interview will be held on May 23 , 2014 at 10:00 AM at NRCPB, LBS Building, Pusa Campus, IARI, New Delhi- 110012. The candidates must bring four copies of biodata (in the prescribed proforma), original certificates, attested photocopies of each of the certificates and an attested copy of recent passport size photograph. No. TA/DA would be given for the appearance in interview. Only the candidates having essential qualification would be entertained for the interviews. Short-listing of candidates based on academic merit and experience will be done in case of large number of applicants.

Advertisement: http://www.nrcpb.org/sites/default/files/Advertisement%20for%20RA%20and%20SRF%20Position.pdf

Installing ELGG on Ubuntu !

Jit — Thu, 25 Nov 2021 01:45:59 -0600

Follow this:

Settings file

Error

Your web server does not have permission to create the settings.php file in your installation directory. You have two choices:

1. Change the permissions on the elgg-config directory of your Elgg installation

2. Copy the file elgg-config/settings.example.php to elgg-config/settings.php and follow the instructions in it for setting your database parameters.

To resolve this --

Change the permision

chmod 777 elgg-config

Web server

Warning

Your server does not support automatic testing of the rewrite rules and your browser does not support checking via JavaScript. You can continue the installation, but you may experience problems with your site. You can manually test the rewrite rules by clicking this link: test. You will see the word success if the rules are working.

create a .httaccess

and provide detail in it

Installation of Elgg

(Note: Elgg requires installing an instance of MySQL.)

Steps to make adjustment and disposal of trial installations easier.

MySQL

At this point, we assume you've set up your MySQL database

Start your mysqld server daemon.
(For the sake of this example, we'll assume we're running on port 9999; you shouldn't actually use this port because only one daemon can run on any port number.)
Login to the server as root user, using the mysql client.
Create a database to store Elgg's tables. We'll call the database elggalpha.
mysql> create database elggalpha;

Grant access to a user — for this example we'll call him/her elggalphauser.

mysql> grant all privileges on elggalpha.* to 'elggalphauser'@'moxie'
    -> identified by 'secretpassword';

Elgg

Type umask 022
Change into your public_html directory (aka folder).
cd public_html
make a directory called elgg
mkdir elgg
Change into the elgg subdirectory of public_html.
cd elgg
download elgg into this directory
you'll end up with a file named
/home/your-user-id/public_html/elgg/elgg-X.X.X.X.zip
(It's not literally X.X.X.X, it might be elgg-1.8.0.1.zip, for example.)
unzip elgg
unzip -q elgg-1.8.0.1.zip
you'll end up with a directory (folder) named
/home/your-user-id/public_html/elgg/elgg-X.X.X.X
make a symbolic link (aka shortcut) to this
ln -s elgg-X.X.X.X alpha
(For example, ln -s elgg-1.8.0.1 alpha)
Give user nobody access to this directory
/usr/misc/bin/acl.sh -r -u nobody elgg-1.8.0.1
create a data directory for elgg (get into your home directory first):
```
cd
mkdir -p elgg/alpha/data
chmod -R 755 elgg/alpha/data
```
Change into the elgg/alpha directory.
cd elgg/alpha
Give user nobody access to this subdirectory data
/usr/misc/bin/acl.sh -u nobody data

In your browser, navigate to your elgg installation
http://moxie.cs.oswego.edu/~your-user-id/elgg/alpha/
You'll have a screen which includes this message:

Welcome

Installing Elgg has 6 simple steps and reading this welcome is the first one!

If you haven't already, read through the installation instructions included with Elgg (or click the instructions link at the bottom of the page).

If you are ready to proceed, click the Next button.

Follow configuration process:

The first screen probably will contain a success message in green and a failure message in pink:
```
Requirements check

Your server failed the requirements check. After you have fixed the below issues, refresh this
page. Check the troubleshooting links at the bottom of this page if you need further assistance.
PHP
```
Your server's PHP satisfies all of Elgg's requirements.
```
Web server
```
We think your server is running the Apache web server. The rewrite test failed and the most likely cause is that AllowOverride is not set to All for Elgg's directory. This prevents Apache from processing the .htaccess file which contains the rewrite rules. A less likely cause is Apache is configured with an alias for your Elgg directory and you need to set the RewriteBase in your .htaccess. There are further instructions in the .htaccess file in your Elgg directory.
```
Database
```
The database requirements are checked when Elgg loads its database.
To correct this, replace the .htaccess file that Elgg created with one that you can edit:
```
cp -ip .htaccess temp-htaccess
rm .htaccess
mv temp-htaccess .htaccess
```
Edit the .htaccess file: Go to approximately line 101 (where it says #RewriteBase /) and add the line:
RewriteBase /~your-user-id/elgg/alpha/
Be sure to save the edited file.
Click the Refresh button.
If this hasn't fixed things, seek professional help.
Click the Next button.

Fill in the parameters appropriate to your MySQL installation.

Database installation

If you haven't already created a database for Elgg, do that now. Then fill in the values below to
initialize the Elgg database.

Database Username

elggalphauser

User that has full priviledges to the MySQL database that you created for Elgg

Database Password

secretpassword

Password for the above database user account

Database Name

elggalpha

Name of the Elgg database

Database Host

^‡

moxie:9999

Hostname of the MySQL server (usually localhost)
‡You might need to use 127.0.0.1:9999 for the host
    if you haven't set up MySQL as we've done.



Database Table Prefix

elgg_

The prefix given to all of Elgg's tables (usually elgg_)

Continue filling in forms as requested.

Configure site

Database has been installed.

We need some information about the site as we configure Elgg. If you haven't created a data directory for Elgg, you need to do so now.

Site Name

My Elgg Site version Alpha

The name of your new Elgg site

Site Email Address

your-user-id@oswego.edu

Email address used by Elgg for communication with users

Site URL

http://moxie.cs.oswego.edu/~your-user-id/elgg/alpha/

The address of the site (Elgg usually guesses this correctly)

Elgg Install Directory

/home/your-user-id/public_html/elgg/elgg.1.8.0.1/

The directory where you put the Elgg code (Elgg usually guesses this correctly)

Data Directory

/home/your-user-id/elgg/alpha/data

The directory that you created for Elgg to save files (the permissions on this directory are checked
when you click Next)

Default Site Access

Public

The default access level for new user created content

Create admin account

Site settings have been saved.

It is now time to create an administrator's account.

Display Name

The name that is displayed on the site for this account

Email Address

Username

Account username used for logging in

Password

Account password must be at least 6 characters long

Password Again

Retype password to confirm

A History of Bioinformatics (in the Year 2039)

Wed, 23 Jul 2014 06:37:51 -0500

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039

Scientists map 17,294 proteins produced in human body

Jit — Thu, 29 May 2014 01:57:55 -0500

Indian scientists missed the genomic profiling bus, but they've more than made up for it by creating the first human proteome map which is an extension of the genomic study. Till now, here is no direct equivalent for the human proteome. But recently two groups present mass spectrometry-based analysis of human tissues, body fluids and cells mapping the large majority of the human proteome.

The Indian scientists working in Bangalore, along with their American counterparts, have mapped more than 17,000 proteins in 30 organs of the human body. Just like the human genome was sequenced around the turn of the millennium, this is an equivalent mapping of the human proteome.

The researcher estimated there are around 20,500 proteins in the human body. These scientists have profiled around 17,294, which account for around 84% of the total proteins. Apart from this, the team also traced around 2,500 of 3,000 proteins that had been categorised as "missing proteins".

The work, done by group of Indian scientists, and Johns Hopkins University, published in the renowned journal Nature ( http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html ). Of the 72 people who worked on the project, 46 are Indians.

Reference:

http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html

http://www.proteinatlas.org/ -The antibody-based Human Protein Atlas programme

http://www.humanproteomemap.org/ -Proteogenomic analysis by identifying translated proteins from annotated pseudogenes, non-coding RNAs and untranslated regions.

https://www.proteomicsdb.org/ -Assembled protein evidence for 18,097 genes in ProteomicsDB

How to sequence the human genome - Mark J. Kiel

Fri, 30 May 2014 13:24:11 -0500

View full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological advances, scientists are now able to know the sequence of letters that makes up an individual genome relatively quickly and inexpensively. Mark J. Kiel takes an in-depth look at the science behind the sequence. Lesson by Mark J. Kiel, animation by Marc Christoforidis.

Genomics and Personalized Medicine

Sun, 01 Jun 2014 23:38:42 -0500

(October 20, 2009) Michael Snyder, Professor of Genetics and Chair of the Department of Genetics at Stanford, discusses advances in gene sequencing, the impact of genomics on medicine, the potential for personalized medicine. and efforts at Stanford to further study these issues. Stanford Mini Med School is a series arranged and directed by Stanford's School of Medicine, and presented by the Stanford Continuing Studies program. Featuring more than thirty distinguished, faculty, scientists and physicians from Stanford's medical school, the series offers students a dynamic introduction to the world of human biology, health and disease, and the groundbreaking changes taking place in medical research and health care. Stanford University http://www.stanford.edu Stanford University School of Medicine http://med.stanford.edu Stanford Continuing Studies http://continuingstudies.stanford.edu Stanford University Channel on YouTube: http://www.youtube.com/stanford

htop explained

Jit — Wed, 06 Jul 2022 01:28:09 -0500

For the longest time I did not know what everything meant in htop.

I thought that load average 1.0 on my two core machine means that the CPU usage is at 50%. That's not quite right. And also, why does it say 1.0?

I decided to look everything up and document it here.

Address of the bookmark: https://peteris.rocks/blog/htop/

Adhoc Bioinformatics Faculty Position @ NIT

Tue, 03 Jun 2014 16:19:52 -0500

NATIONAL INSTITUTE OF TECHNOLOGY, DEPARTMENT OF BIOTECHNOLOGY, WARANGAL – 506 021, Andhra Pradesh

No.NITW/BT/2014/adhoc

APPLICATIONS ARE INVITED FOR THE APPOINTMENT OF ADHOC FACULTY ON CONTRACT BASIS IN THE DEAPARTMENT OF BIOTECHNOLOGY

Period of Contract: Initially the appointment is for one semester i.e., from July 2014 up to December 2014 only.

Essential Qualifications:

i) B. Tech or equivalent in Biotechnology/ Industrial Biotechnology/ Biochemical Engineering / Chemical Engg. Or M. Sc in Microbiology/ Botany/ Zoology/ Biochemistry/Biotechnology and ii) M. Tech or equivalent in Biotechnology/Industrial Biotechnology/Bioinformatics

Integrated M. Tech in Biotechnology/Industrial Biotechnology/ Bioinformatics

Candidates must possess First class (60% aggregate marks or 6.5 CGPA) at B. Tech/ M. Sc and M. Tech.

Desirable: Ph. D Pay Package: All selected candidates shall be eligible for a consolidated pay of Rs.30, 000/- per month. Candidates with Ph. D shall be eligible for an additional amount of Rs.5, 000/- per month.

How to apply : Applications on plain paper with attested photocopies of certificate and bio data along with justification for eligibility should reach to the Head, Department of Biotechnology, National Institute of Technology, Warangal AP 506004 in the form of soft or hard copy on or before 21st June 2014 email : biotech_hod@nitw.ac.in

Intimation: No separate call letters will be sent to the candidates. All the eligible candidates will be notified in the institute web site on 23rd June 2014. All the eligible candidates are requested to report for the interview to the Head, Department of Biotechnology at 9:00 AM on 27th June 2014

Joining: Selected candidates will be informed and they are expected to join immediately.

http://www.nitw.ac.in/nitw/announcements/2014/Bio-Adhoc%20Advt.%20May-2014.pdf

BioCircos.js is an open source interactive Javascript library to interactive display biological data on the web

Jit — Fri, 19 Jan 2018 15:03:51 -0600

BioCircos.js is an open source interactive Javascript library which provides an easy way to interactive display biological data on the web. It implements a raster-based SVG visualization using the open source Javascript framework jquery.js. BioCircos.js is multiplatform and works in all major internet browsers (Internet Explorer, Mozilla Firefox, Google Chrome, Safari, Opera). Its speed is determined by the client’s hardware and internet browser. For smoothest user experience, we recommend Google Chrome.

BioCircos.js provides SNP, CNV, HEATMAP, LINK, LINE, SCATTER, ARC, TEXT, and HISTGRAMmodules to display genome-wide genetic variations (SNPs, CNVs and chromosome rearrangement), gene expression and biomolecule interactions. BioCircos.js also provides BACKGROUND module to display background and axis circles. Tooltips showing detailed information of SVG elements are also provided.

Demo

Address of the bookmark: http://bioinfo.ibp.ac.cn/biocircos/document/index.html