BOL: Related items

Google Genomics

Tenzin Paul — Thu, 18 Dec 2014 11:05:42 -0600

Explore genetic variation interactively. Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.
Process big genomic data easily. Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.
Use Google's infrastructure and big data expertise. Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.
Support emerging global standards. Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

Address of the bookmark: https://cloud.google.com/genomics/

Bioinformatics Made Easy Search: Bioinformatics tools and run genomic analysis in the cloud

Rahul Nayak — Thu, 20 Aug 2015 02:21:20 -0500

InsideDNA makes hundreds of bioinformatics tools immediately available to run via an easy-to-use web interface and allows an accurate search across all functions, tools and pipelines.

With InsideDNA, you can upload and store your own genomic/genetic datasets in a limitless cloud space, and instantly analyze it with a powerful compute instance, without any tool installation or set up hassle.

More at https://insidedna.me/

Address of the bookmark: https://insidedna.me/

Binding Site Prediction in Protein !

Poonam Mahapatra — Wed, 25 Apr 2018 04:35:57 -0500

The interaction between proteins and other molecules is fundamental to all biological functions. In this section we include tools that can assist in prediction of interaction sites on protein surface and tools for predicting the structure of the intermolecular complex formed between two or more molecules (docking).

Pockets Identification

CASTp

Automatic Identification of pockets and cavities in proteins structure, and quantitation of their volumes using Delaunay triangulation. Available also as PyMOL plugin

Pocket-Finder

Automatic identification of pockets and cavities in proteins structure, and quantitation of their volumes.

PocketPicker

Grid-based technique for the analysis of protein pockets. PocketPicker available as a plugin for PyMOL

Binding Site Prediction

ConSurf

Identification of functional regions in proteins by surface-mapping of phylogenetic information

CRESCENDO

Identification protein interaction sites. It uses sequence conservation patterns in homologous proteins to distinguish between residues that are conserved due to structural restraints from those due to functional restraints.

Ligand Binding Sites

3DLigandSite

The server utilizes protein-structure prediction to provide structural models of the binding site. Ligands bound to structures are superimposed onto the model and use to predict the binding site.

FINDSITE

A threading-based method for ligand-binding site prediction and functional annotation based on binding-site similarity across superimposed groups of threading templates.

LIGSITE^csc

Prediction of binding site by pocket identification using the Connolly surface and degree of conservation

metaPocketA meta server for ligand-binding site prediction. metaPocket use LIGSITE^csc, PASS, Q-SiteFinder and SURFNET

Bioinformatics web development course

Jit — Wed, 06 Nov 2019 20:42:48 -0600

This web development course, targeted at Biology and Bioinformatics students, aims at teaching from scratch all the skills needed to setup a fully working Linux web server and to develop and deploy web applications for Bioinformatics.

No previous programming knowledge is assumed. By following this tutorial you will learn the fundamental concepts of programming by using scripting languages: variables, types, arrays, cycles, conditional statements, functions, objects, regular expressions, files reading and manipulation et-cetera.

Address of the bookmark: http://www.cellbiol.com/bioinformatics_web_development/introduction/

Research Associate Bioinformatics in IISc Recruitment 2020

Tue, 23 Jun 2020 21:53:34 -0500

Research Associate Bioinformatics in IISc Recruitment 2020

Essential Qualifications: Ph.D. (Bioinformatics/ Biophysics/ Biotechnology or any other stream of biological/ physical sciences) with a minimum of two publications in reputed peer reviewed journals in the area of structural bioinformatics or biophysics or biomolecular modeling/ simulation.

Job description: Development of bioinformatics tools and algorithms/software for structure based analysis of biomolecular systems. Programmatic access to major biomolecular databases using APIs Knowledge based prediction and analysis of biomolecular structure, function and interactions. Docking/simulations for inhibitor design.

Desirable Qualifications (Research Associate/s): i) Strong computer programming skills (in Python/PERL/PHP or C++ or object oriented database management systems like MySQL etc or scripting languages under LINUX/UNIX environment).

ii) Extensive experience in computational analysis of biomolecular structure/interactions and usage of advanced biomolecular simulation softwares. iii) Adequate knowledge of major databases, webservers and softwares in the area of biomolecular structure/function and drug design. iv) Familiarity with Parallel Programming environments and experience in usage of high-end HPC clusters.

The candidates must highlight their experience in above mentioned fields/topics in their CV. Initial appointment will be for a period of 1 year, subject to extension after review of performance.

Emoluments: As per DST, GOI norms and commensurate with experience.

More at https://www.iisc.ac.in/positions-open/

ICMR Scientist Jobs For Biotech/Life Science/Biology & Bioinformatics

Tue, 10 Nov 2020 18:45:49 -0600

CMR welcomes on-line applications up to 5th December 2020 till 5:30 PM to fill out the vacancies of 42 Scientist’ E’ (Medical), 01 Scientist ‘E’ (Non-Medical), 16 Scientist ‘D’ (Medical) and also 06 Scientist ‘D’ (Non-Medical) from Indian Citizens for appointment on regular basis under Direct Recruitment with all India transfer liability under the Council.

Post I

Name of the Post: Scientist-E (Non-Medical)

Number of positions: One

Upper Age limit: 50 years

Post II

Name of the Post: Scientist-D (Non-Medical)

Number of positions: Six

Upper Age limit: 45 years

Fee:

Application Fee of Rs. 1500/- (Rupees one thousand five hundred only) is needed. SC / ST / Women/ PWD/ EWS applicants are exempted from application fee. Application Fee is to be paid by candidates through online web link given up the application. Application fees when paid will certainly not be reimbursed under any situations.

How to apply:

i) Candidates should apply online on https://recruit.icmr.org.in. A separate application needs to be submitted for every post, with the required application fee.

ii) Following self-attested documents are required to be uploaded together with the application:
a) Proof of Date of Birth.
b) Educational qualifications.
c) Experience.

More at https://recruit.icmr.org.in/assets/uploads/advertisement/ICMR_Advertisement_06112020.pdf

Check Linux server configuration !!

Rahul Nayak — Tue, 06 May 2014 01:10:57 -0500

Bioinformatician uses servers for computational analysis. Sometime we need to check the server details before running our programs or tools. Here I am showing some basic commands using them you can gather the system/server information.

To check what version of Operating System is installed on the server you can use the following commands:-
=================================================================
1.cat /etc/issue
[root@localhost ~]# cat /etc/issue
Red Hat Enterprise Linux Server release 5.5 (Tikanga)
Kernel \r on an \m

2.cat /etc/redhat-release
[root@localhost ~]# cat /etc/redhat-release
Red Hat Enterprise Linux Server release 5.5 (Tikanga)

3.lsb_release -a
[root@localhost ~]# lsb_release -a
LSB Version:    :core-3.1-ia32:core-3.1-noarch:graphics-3.1-ia32:graphics-3.1-noarch
Distributor ID: RedHatEnterpriseServer
Description:    Red Hat Enterprise Linux Server release 5.5 (Tikanga)
Release:        5.5
Codename:       Tikanga

To check whether the operating system is 32 or 64bit:-
================================
# uname -i
[root@localhost ~]# uname -i
i386
(i386 represents that server is having 32bit operating system)

[root@localhost ~]# uname -i
x86_64
(x86_64 represents that server is having 64bit operating system)

To see the processor/CPU information:-
=============================
# cat /proc/cpuinfo
[root@localhost ~] cat /proc/cpuinfo
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 15
model name      : Intel(R) Xeon(R) CPU            5130 @ 2.00GHz
stepping        : 6
cpu MHz         : 1995.087
cache size      : 4096 KB
physical id     : 0
siblings        : 2
core id         : 0
cpu cores       : 2
apicid          : 0
fdiv_bug        : no
hlt_bug         : no
f00f_bug        : no
coma_bug        : no
fpu             : yes
fpu_exception   : yes
cpuid level     : 10
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe nx lm constant_tsc pni monitor ds_cpl vmx tm2 ssse3 cx16 xtpr lahf_lm
bogomips        : 3990.17
(Here processor number 0 indicates that the system is having one process(processor number starts with zero))

To check memory information:-
===========================
# free -m
[root@localhost ~]# free -m
             total       used       free     shared    buffers     cached
Mem:          5066       3513       1552          0        612       2319
-/+ buffers/cache:        582       4484
Swap:         1983          0       1983

# cat /proc/meminfo
[root@localhost ~]# cat /proc/meminfo
MemTotal:      5187752 kB
MemFree:       1639300 kB
Buffers:        627024 kB
Cached:        2374944 kB
SwapCached:          0 kB
Active:        2458788 kB
Inactive:       920964 kB
HighTotal:     4325164 kB
HighFree:      1561936 kB
LowTotal:       862588 kB
LowFree:         77364 kB
SwapTotal:     2031608 kB
SwapFree:      2031608 kB
Dirty:             704 kB
Writeback:           0 kB
AnonPages:      377892 kB
Mapped:          35328 kB
Slab:           153036 kB
PageTables:       6316 kB
NFS_Unstable:        0 kB
Bounce:              0 kB
CommitLimit:   4625484 kB
Committed_AS:   977132 kB
VmallocTotal:   116728 kB
VmallocUsed:      4492 kB
VmallocChunk:   112124 kB
HugePages_Total:     0
HugePages_Free:      0
HugePages_Rsvd:      0
Hugepagesize:     2048 kB

To check the model and serial name of the server:-
=======================================
[root@localhost ~]# dmidecode | egrep -i "product name|Serial number"
Product Name: PowerEdge R710
Serial Number: AB8CDE1


To check the host name:-
=====================
[root@localhost ~]# uname -n
localhost

[root@localhost ~]# hostname
localhost

To check the kernel version:-
========================
[root@localhost ~]# uname -r
2.6.18-238.9.1.el5PAE

Postdoc position at Centre Méditerranéen de Médecine Moléculaire

Sun, 06 Jul 2014 11:23:06 -0500

The research group of Dr. Michele Trabucchi at the Centre Méditerranéen de Médecine Moléculaire (C3M) at INSERM U1065 (University of Nice Sophia-Antipolis, France) is seeking candidates for a Postdoctoral fellow position to start on October 2014 for 3 years funded by FRM (Fondation pour la Recherche Médicale).
The broad interest of the lab is in understanding the expression control and function of small RNAs in activated myeloid cells (visit our webpage to check research interests and publications of the group : http://www.unice.fr/c3m/EN/Equipe10.html ).

The work will focus on the functional studies of small RNAs by using next-generation sequencing approaches.

Candidates should hold a Ph.D. degree and have strong background in bioinformatics.
The University of Nice Sophia-Antipolis provides a wide range of facilities and training essential for biomedical research.
Interested applicants should send a PDF with a cover letter stating research interests and qualifications, an updated CV, a summary of previous research experience and contact information for two references to Michele Trabucchi ( mtrabucchi@unice.fr )

Research Associate at Indian Institute of Chemical Technology (IICT), Hyderabad

Thu, 07 Aug 2014 01:55:21 -0500

Indian Institute of Chemical Technology (IICT), Hyderabad, a constituent of CSIR is a leading research Institute in the area of chemical sciences. The core strength of IICT lies in Organic Chemistry, and it continues to excel in this field for over six decades. The research efforts during these years have resulted in the development of several innovative processes for a variety of products necessary for human welfare such as drugs, agrochemicals, food, organic intermediates, adhesives etc. More than 150 technologies developed by IICT are now in commercial production.

CSIR-IICT is conducting Walk in Interview for the following position on a purely temporary basis for the sponsored project "GENESIS (BSC-0121) at 10.00 AM on 19th August 2014 at IICT, Hyderabad

Position : Research Associate
No of Post : One
Desired Profile : PhD in computation biology or M.Tech in Computational Biology with three years experience in relevant subject and atleast one research paper in SCI journal

Experience : Knowledge in vector and vector borne disease, disease modeling, GIS mapping and modeling.
Age : 35 years
Stipend : Rs 22000/- + HRA

Eligible candidate may download the application form from our website http://www.iictindia.org and appear for interview along with the duly filled in application form supported by bio-data and one set of attested photo copies of certificates of educational qualification, age, experience, caste, latest photograph and the cadndidates are required to bring all the original certificates for verification

Walk in Interview : 19.08.14

Project Assistant II Jobs opportunity in National Chemical Laboratory (NCL) on temporary basis

Fri, 06 Nov 2015 01:36:16 -0600

No. Bio/NCIM/3

Project Assistant II Jobs opportunity in National Chemical Laboratory (NCL) on temporary basis

Project Code No. : GAP312626

Title of the Project : Microbial ecology and distribution of geochemical cycling genes in an hot spring ecosystem

No. of Post : 01

Qualifications : M.Sc./B.Tech/M.Tech in Computational biology/ Bioinformatics from recognized university with minimum 60 % marks (aggregate)

Desirable : Good knowledge of computational skills, Linux (command line and GUI) and Unix; Perl / Python / R /C-programming. Practical knowledge of analysis of Next generation sequence datasets (amplicon sequencing, whole metagenome, and complete genome sequencing) with reference to microbes. Analysis and statistical validation of NGS data generated from different chemistry platforms. Some wet-lab experience in microbial system would be an added advantage as project involves some travel.

Emoluments : Rs. 16,000/-

Age Limit : 28 years
How to apply

The application with the above information duly signed together with photo-copies of relevant certificates/testimonials should be addressed to : The Head, NCIM Resource Centre (Attn Dr. M.S. DHARNE), National Chemical Laboratory, Pune 411 008, so as to reach on or before 16th November 2015.

More at http://www.ncl-india.org/files/JoinUs/JobVacancies/TemporaryJobs.aspx?menuid=ql6&childmenustripid=divSubQL6