BOL: Related items

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

A National Workshop on "DNA Barcoding and Phylogenetics" 09 th – 12 th August, 2017 @ Andhra University, Visakhapatnam, A.P., India

M JAGANNATH — Wed, 26 Jul 2017 00:37:20 -0500

DNA Barcoding is an emerging global standard for identifying species using gene sequences, and it has far reaching applications for society and the study of biodiversity on Earth. DNA Barcoding began during
recent decades with the proposal that organisms could be assigned to their correct species using a short gene sequence from a standardized position in the genome. By using genetic data rather than morphological features, barcoding can identify specimens that challenge the most expert taxonomist: larval forms, eggs, damaged or partial specimens (including gut contents and fecal matter), and derivative forms (e.g., fish filets). Since its introduction, barcoding has proven effective as an identification system for a wide range of taxonomic groups and for varied applications of importance to science and society.
The current Workshop aims to introduce about the current emerging trends and applications of Molecular
Phylogenetics and Evolution studies and to provide hands on training on molecular biology and bioinformatics tools in Molecular Phylogenetics research.

For registration Kindly follow the Link

http://andhrauniversity.edu.in/webnew/admin/docs/Broucher-for-National-workshop-Aug-2017-18072017.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

JRF/SRF at University of Calcutta

Fri, 31 Oct 2014 08:53:10 -0500

Applications are invited to appear at a walk-in-interview for one post of Junior Research Fellow in the DBT(DBT Twinning NER) sponsored project entitled “Protein folding kinetics is a selection force on shaping codon usage bias in the high expression genes” in the room of the HOD, Department of Biotechnology and the Coordinator, DR. B. C. Guha Centre for Genetic Engineering and Biotechnology, University College of Science, 35 Ballygunge Circular Road, Kolkata 700019 on the 12th November, 2014 at 3:00 p.m.

Essential qualifications: First class M. Sc. in any branch of life sciences and qualified CSIR-UGC NET/GATE Examination.

Desirable qualifications: Practical experience in biochemical and biophysical studies of proteins

Emoluments: as per DBT norms

The project is tenable for two years, initially for one year.

Age: Below 28 years (relaxable in the case of SC/ST/OBC/women candidates)

Candidates are requested to bring two sets of complete applications on plain paper furnishing bio-data and copies of attested certificates along with originals (for verification) on the date of interview.

No TA/DA is admissible for candidates appearing at the interview.

Dr. Rajat Banerjee
Assistant Professor
Department of Biotechnology and
Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology
University College of Science
35, Ballygunge Circular Road
Kolkata 700019

Advertisement: www.caluniv.ac.in/news/jrf_biotech_2.pdf

Opening for RA/extended SRF in Bioinformatics project by DBT at Bose Institute

Sun, 01 Mar 2015 00:50:18 -0600

The institute has evolved over the years into a multi-disciplinary research organization with stress on fundamental research in its pursuit of advancement of knowledge in Science and technology and at the same time developing highly competent and able scientific manpower for the country. The institute has on its staff highly qualified and experienced scientists working in the field of Biological, biochemical, Chemical and Physical sciences placed in long established departments of Physics, Chemistry, Botany, Microbiology, Biochemistry, and Biophysics, and the research sections on plant Molecular & Cellular Genetics, Animal Physiology, Immunotechnology and Environmental science

Walk-in-Interview will be held on 04th March 2015 at 11.30 A.M. in the Bio- Informatics Centre of Bose Institute, P-1/12, C.I.T. Scheme VII-M, Kolkata- 700054 for two (02) positions of Research Associate/ Extended Senior Research Fellow in the DBT sponsored following two projects running under the CoE- Bioinformatics under the guidance of Prof. Pinakpani Chakrabarti, Bioinformatics Centre.

Position : RA/SRF
Project title : 1. "Centre of Excellence (CoE) in Bioinformatics at Bose Institute”,2. Project entitled “Setting up of National Facility on Interactive Graphysics Computer System (IGCS) for Biomolecular Modeling, Molecular Dynamics & Structures”

Desired Profile : Ph.D degree in Biological or Chemical Sciences with in-depth understanding of protein structure and dynamics for R.A. position.Those who have submitted thesis can be considered for Extended SRF position
Preferred : Knowledge of computer programming and bioinformatics softwares.
Stipend : For R.A- Rs. 22,000/- p.m., plus admissible H.R.A. and Medical benefit. For Extended SRF - Rs. 20,000/- p.m., plus admissible H.R.A.and Medical benefit.
Age : For R.A- Below 35 years; For Extended SRF - Below 33 years
Interested and eligible candidates should appear before the Selection Committee with atyped application addressed to the Sr.Prof. & In-Charge, Registrar's Office, Bose Institute, P- 1/12, CIT Scheme VII-M, Kankurgachi, Kolkata-700054 along with Bio-data giving details of qualification i.e. examination passed, year, division, percentage of marks from Secondary onwards with attested copies of Certificates, Mark-Sheet and testimonials. The candidates should also bring the original mark-sheets, certificates etc. at the time of Interview.

Walk in Interview : 04.03.15

More at http://www.boseinst.ernet.in/ADVT/14/p_34.pdf

Research Associate Biotechnology/JRF/Lab. Assistant Indian Institute of Vegetable Research (IIVR) - Varanasi, Uttar Pradesh

Wed, 11 Mar 2015 08:59:27 -0500

F. No.: 2-19/2011-Adm.I

Research Associate Biotechnology /JRF / Lab. Assistant recruitment in Indian Institute of Vegetable Research

Project:
Genomics assisted selection of Solanum chilense introgression lines for enhancing drought tolerance in tomato
Post Name : Research Associate
Qualification : Ph.D in Biotechnology/ Bioinformatics/Genetics & Plant Breeding. M. Tech in Computer Science with at least one research paper in science citation indexed journal. Desirable: Experience in bioinformatics and next generation sequence data handling. Familiarity in Linux, R, Perl/Phython or other programming languages. Willingness to travel to European partner centers.

Pay Scale : Rs. 36000 for 1st and 2nd year as per rules for Research Associate. Rs. 25000/- for 1st and 2nd year and Rs. 28000 as per rules for Junior Research Fellow. Rs. 7000/- for Lab. Assistant.

Age : Not more than 35 years for Men and 40 years for Women (Relaxable for SC/ST/OBC/PH candidates as per rules) for Research Associate/ Junior Research Fellow. Minimum age will be 21 years and maximum age will be 45 years (Relaxable for SC/ST/OBC/PH candidates as per rules) for Lab.Assistant.

More at http://iivr.org.in/Job%20Oppurtunities/RA20.03.2015.pdf

ICAR project RA position @ Institute of Bioinformatics (IOB) Bangalore

Tue, 22 Sep 2015 23:41:31 -0500

Applications are invited for the post of Research Associate (RA) in the ICAR project on "Lactation stress associated postpartum anestrus SNP array in buffaloes". We are looking for a motivated candidate for handling Next Generation sequencing data analysis with a strong background in bioinformatics and programming.

The position is open for immediate appointment and available for two years and then extendable for additional one year. The applicant will be appointed as Research Associate based on qualifications as detailed below:

Research Associate:

-Master’s degree with bioinformatics with at least 2 years of research experience in Next Generation sequencing data analysis as evidence from Fellowship/ Associateship / Training / other engagements.

-Familiarity with bioinformatics tools, database development, programming skills

-Minimum 1 publication in any peer reviewed journal

Salary will be as per ICAR rules and guidelines. Application will be shortlisted based on CV, reference letters from mentors and telephonic interview. Candidates will be called for a personal interview at Bangalore before appointment. No travel expense will be provided for attending interview at Bangalore.

Interested candidates may send a Letter of Interest and CV by email to: keshav@ibioinformatics.org before September 29, 2015.

Project Fellow at Indian Institute of Chemical Biology (IICB)

Tue, 22 Sep 2015 23:47:35 -0500

Advertisement No. : R&C/CD/427/2015 ,Vacancy Code: 4271501

Project Fellow Bioinformatics recruitment in Indian Institute of Chemical Biology (IICB) purely temporary

Name of the Project: "Genomics and Informatics Solutions for Integrating Biology(Genesis)".

No. of Vacancies: 1

Qualification required : M.Sc in Bioinformatics with 55% Marks.

Experience (Desirable): Candidate should be well versed with sequencing data analysis,assembly and annotation of whole genome sequence. Experience in transcriptional data analysis is also preferred.

Age Limit : 28 Years

Stipend : Rs.16000
How to apply
Interested candidates may appear for the walk-in-interview to be held on 28.09.2015 from 11.00 a.m. in the Red Carpet Room with the following documents self attested copy - (1) Matriculation Certificate in support of your date of birth, (2) Degree/Diploma Certificate, (3) Original reprints of all testimonials regarding educational qualification, (4) No Objection Certificate from the employer if employed, (5) Final Mark Sheet of M.Sc. Examination, (6) One Passport size photograph.

http://www.career.iicb.res.in/Recruitment%20Notice.php

LAST

Archana Malhotra — Wed, 09 Mar 2016 14:27:01 -0600

LAST can:

Handle big sequence data, e.g:
- Compare two vertebrate genomes
- Align billions of DNA reads to a genome
Indicate the reliability of each aligned column.
Use sequence quality data properly.
Compare DNA to proteins, with frameshifts.
Compare PSSMs to sequences
Calculate the likelihood of chance similarities between random sequences.
Do split and spliced alignment.
Train alignment parameters for unusual kinds of sequence (e.g. nanopore).

Address of the bookmark: http://last.cbrc.jp/

Genome Stability Laboratory

Mon, 07 Mar 2016 04:16:32 -0600

The bakers yeast, Saccharomyces cerevisiae is an ideal model organism to understand mechanisms of meiotic chromosome segregation. In S. cerevisiae and in mammals, the majority of meiotic crossovers are formed through a highly conserved MSH4p-MSH5p, MLH1p-MLH3p dependent pathway. We are interested in charactering the role of these complexes in crossover formation and distribution among all homolog pairs. Errors in this process are linked to congenital birth defects in humans such as Down's syndrome.Our laboratory is also interested in understanding the effect of genetic background on mutation rate variation using S. cerevisiae as a model. These studies are relevant for understanding cancer progression, genome evolution and architecture. We use high- throughput genomic methods as well as classical genetics to achieve these aims.

More at http://faculty.iisertvm.ac.in/~nishantkt/index.html