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Bio Saga

Monday, January 31, 2011

National level Workshop in Chemoinformatics

26th- 27th Feb 2011

Workshop groups will study problems with hands-on examples using computational chemistry methods and discuss issues highlighted by examples and Case Studies presented by instructors. A Case Study set with a focus on chemical database creation and filtering drug like compounds will be used to link all workshop activities throughout the workshop.
  • Hands on training on commercial softwares of Drug discovery
  • Application of Chemoinformatics in drug discovery
  • Interaction and guidance from eminent scientist from NCL
  • Training from industry experts from Chemoinformatics domain.
  • Analyzing chemical fingerprint
  • Generating Knowledge from structure and different chemical databases
  • Using various chemical structure drawing and visualization tools
  • Digitizing your chemical Data.
  • Storing molecules in wide array of format
  • Awards for top 3 groups
For any queries contact:

RASA Life Science Informatics
301, 3rd Floor, Dhanashree Apartment,
Opposite Chittaranjan Vatika, Model Colony,
Shivaji Nagar, Pune - 411016.
Tel: 02065600408, 02025665752 or email us at workshop@rasalsi.com

For downloading workshop broacher please visit www.rasalsi.com

Tuesday, January 25, 2011

WORKSHOP- COMPUTATIONAL APPROACHES IN BIOLOGICAL DATA MINING

A Workshop on Computational Approaches in Biological Data mining is being organised by the
Unit Of Simulation and Informatics, Indian Agricultural Research Institute, New Delhi.

The topics to be discussed are:-
  • Introduction to Biological databases 
  • Biological data mining 
  • Concept and application of machine learning techniques in bioinformatics 
  • Tools and techniques for bio-molecular prediction 
  • Future directions in biological data mining.
 Dates:- March 23rd-25th, 2011.

Application deadline:- February 25th, 2011.

Do you wish to know more?


2nd INTERNATIONAL CONFERENCE on BIOINFORMATICS AND SYSTEMS BIOLOGY

The genome – sequencing and structural genomics efforts worldwide have contributed to huge data on protein sequences and novel protein folds. However, there still remains a wide gap between the number of known protein sequences and three dimensional structures. The conference will deal to protein fold prediction, comparative protein modelling, secondary structure prediction, protein dynamics and simulations, ab-initio prediction and the validation of protein models and various aspects of structure determination and analysis by X – ray crystallography.

    Paper submission open December 2, 2010
    Paper submission deadline January 20, 2011
    Paper acceptance decision January 28, 2011
    Poster submission open December 30, 2010
    Poster submission deadline January 28, 2011
    Poster acceptance decision January 31, 2011
    Registration open December 2, 2010
    Early-bird registration upto January 31, 2011
    Conference Feb 16 - 17, 2011

Friday, January 21, 2011

Bioinformatics National Certification (BINC) Examination

JNU New Delhi, on behalf of Department of Biotechnology, Government of India, will conduct the BINC examination on February 26-27, 2011. The objective of this examination is to certify bioinformatics professionals, trained formally as well as self-trained. 

Registration is open from 13-12-2010 to 03-02-2011. After 5 years of conducting this examination by University of Pune, recently in 2010, JNU New Delhi has been identified as a nodal agency by the Department of Biotechnology, Govt. of India to coordinate this examination along with six centres namely, Pune University, Pune; Anna University, Chennai; West Bengal University of Technology, Kolkata; Institute of Bioinformatics & Applied Biotechnology, Bangalore; North-Eastern Hill University, Shillong and University of Hyderabad, Hyderabad.

In the BINC 2009 examination, 519 candidates appeared out of which 30 candidates were certified. This year DBT has agreed to fund Research fellowships for all the BINC qualified Indian nationals to pursue Ph.D. in Indian Institutes/Universities. Note that the candidate must possess a postgraduate degree(or equivalent) & meet the criteria of the institutes/universities in order to avail research fellowship. In addition, cash prize of Rs. 10,000/- will be awarded to the top 10 BINC qualifiers. 

Graduates and above in any science, agriculture, veterinary, medicine,
pharmacy, engineering and technology are eligible to appear for the
examination. They need not have any formal training, diploma or
certificate in bioinformatics.
 
Last date of registration: 3 February 2011
Date of examination: 26–27 February 2011
Organised by-Department of Biotechnology, Government of India, New Delhi and School of Computational and Integrative Sciences, JNU, New Delhi
 
Please refer to the link for further informations-http://binc.scisjnu.ernet.in/


Thursday, January 20, 2011

Tasmanian Devil genomes sequenced as a step towards their conservation

Using genome sequencing and other strategies, researchers from Pennsylvania State University and elsewhere are finding genetic clues that they say may be useful for selecting Tasmanian devils for breeding programs aimed at saving the animals from extinction.
The team used Roche 454 technology to do de novo sequencing of two Tasmanian devil genomes, Penn State biochemistry and molecular biology researcher Stephan Schuster said during Roche Applied Science workshop at the Plant and Animal Genomes conference this week.
By looking at SNP data in the nuclear and mitochondrial genomes of Tasmanian devils, he explained, the team is tracking down informative markers that they believe may be useful for gauging genetic diversity and managing Tasmanian devil populations through more tailored breeding programs.

Workshop - "In-silico Drug Discovery Based on the Integration of Bioinformatics and Chemoinformatics"

The Workshop

Drug discovery is an expensive and time taking process and therefore new approaches based on chemoinformatics and bioinformatics are being adopted.The knowledge of the 3D structures of protein targets is now playing a major role at all stages of drug discovery. The distinct nature of biological and chemical information requires the integrated capabilities of both bioinformatics and chemo-informatics to decipher existing and hidden relationships. Bioinformatics and chemo-informatics have largely evolved independently from biology and chemistry. Cheminformatics is an inter-disciplinary subject of storage, processing and retrieval of chemical information. Bioinformatics and chemoinformatics have significantly assisted in lead optimization, fingerprinting, pharmacophore designing, target identification, QSAR and their application can lead to discovery of new molecules. Molecular modeling using 3D graphics and optimization techniques helps the scientists to understand how drugs bind to proteins in the body. Classically, protein structure has been exploited in lead optimization, a process that uses structure to guide the chemical modification of a lead molecule to give an optimized fit in terms of shape, hydrogen bonds and other non-covalent interactions with the target. Protein structure can also be used in target identification and selection.
Any homologue of identified known structure can be modeled using a variety of comparative modeling procedures. Lead modification is used for modification in order to improve desired pharmacological properties. A small part of a lead compound may be involved in the appropriate interaction. The relevant groups on a molecule that interact with receptor and are responsible for activity are collectively known as pharmacophore.

The workshop aims:
  1. To familiarize the researchers and students with applications of bioinformatics and chemoinformatics in drug discovery.
  2. To familiarize participants with current advances in the macromolecule structure prediction, including protein structure, protein folding, molecular dynamics and simulation.
  3. To acquaint participants with in- silico chemical and structural fingerprinting, designing and preparation of lead molecules for drug designing and various tools and techniques to bioinformatics and chemoinformatics.
Objectives

The participants of the workshop will be accessing online resources of macromolecule libraries, sketching chemical compounds and building 3-D molecules, drug designing. They would also learn about prediction and analysis of various properties of compounds, bimolecular and structure prediction and visualization and analysis. The practical knowledge gained through this workshop will help them in enhancing their skills in utilizing tools for their application in basic and industrial research and employment potential.

Workshop Contents

The workshop will consist of lectures, group discussions, case studies, exchange & sharing of experience on :
  • Bioinformatics and its application
  • Biological Databases
  • Functional Genomics and Proteomics
  • Structural Bioinformatics
  • Proteins 3-D Structure Prediction
  • Drug Designing & Case study
  • Science involved in disease target identification
  • Pocket/ Active site identification
  • Lead identification and optimization
  • In-silico generation of novel ligand molecules
  • Target ligand docking
  • 3-D Quantitative Structure Activity Relationships
  • Rational drug discovery
  • RNA Interference
Who should attend?

Scientists / Research fellows (National Laboratories & Universities) and Graduate / Post graduate students in Engineering / Biological / Chemical sciences/ Medical discipline.

Duration

February 23 – 25, 2011

Venue

Biotech Park,
Sector-G, Jankipuram,
Near Biotech Square, Kursi Road,
Lucknow-226021, (U.P.), India.

Number of Participants

SEATS ARE AVALABLE.

Registration Fee

Rs 2,000/- per participant. The registration fee includes lectures/presentation handouts, stationary, local transportation, lunch and tea. Fee is to be paid through bank draft drawn in favour of “CEO, Biotech Park, Lucknow”, Completed registration form along with the fee should reach, CEO, Biotech Park on or before February 21, 2011.


Wednesday, January 19, 2011

India, UK step up biotech links

In continuation to the earlier story UK and India Partner on $32M Agriculture Program The life sciences industry leaders from both India and UK came together in London in early December to strengthen the business ties between the nations in this sector

A delegation of biotech industry leaders from India traveled to the UK to meet with their counterparts to renew and forge new ties for a week in December. The Indian delegation’s visit to London was facilitated by the government agency, UK Trade & Investment (UKTI). 


The visit certainly opened the eyes of Indian entrepreneurs to the opportunities for strategic collaboration with their UK counterparts. Many formal agreements can be expected in 2011.

Tuesday, January 18, 2011

UK and India Partner on $32M Agriculture Program


The UK's Biotechnology and Biological Sciences Research Council will manage a new grant program that will use £20 million ($31.7 million) to fund a range of research projects in the UK and India aimed at improving food security in the developing world, according to BBSRC.
Funded by BBSRC, the Bill and Melinda Gates Foundation, the UK Department for International Development, and the Indian Department of Biotechnology, the new initiative will award grants to support research approaches, which could include genomics, to improve the sustainability of food crops.
The funding under the Sustainable Crop Production Research for International Development Initiative will be awarded to research teams that can show how their work may improve food security and boost crop sustainability within the next five-to-10 years.
The new initiative will place particular emphasis on improving the "sustainable production of staple food crops across sub-Saharan Africa and South Asia," Sam Dryden, director of Agricultural Development at the Bill and Melinda Gates Foundation, said in a statement.
"These include cassava, maize, rice, sorghum and wheat. By placing significant emphasis on these crops the initiative partners expect to be able to improve food security and quality of life for the largest possible number of people," Dryden explained.
According to Stephen O'Brien, UK Parliamentary Under-Secretary of State for International Development, millions in the two regions depend on staple crops such as maize and rice as a source of food and income. "Reducing the unpredictability of growing crops helps to ensure that the poorest countries are able to feed their people, cope with sudden global food price changes, and ultimately boost economic growth," he said.
BBSRC Chief Executive Douglas Kell added that "Scientists and organizations across the world have the capabilities and expertise to make a real difference in meeting the global food security challenge but no single organization or country can do this on its own."

Sequence assembly and annotation of the first citrus genomes

Researchers from the International Citrus Genomics Consortium announced this weekend at the Plant and Animal Genome (PAG) XIX conference in San Diego, California the availability of the sequence assembly and annotation of the first citrus genomes, the sweet orange (Citrus sinensis) and the Clementine mandarin (Citrus clementina). The sweet orange genome was sequenced and analyzed in joint collaboration between the University of Florida, DOE Joint Genome Institute, the Georgia Institute of Technology and 454 Life Sciences, a Roche Company, using the high-throughput GS FLX System. Funded in part by the Florida Citrus Production Research Advisory Council, a citrus grower industry organization, the project is expected to assist geneticists and breeders improve these important fruit crops. The assembled and annotated genomes have been added to the publicly available database Phytozome.net, a project of the DOE JGI and the Center for Integrative Genomes.

Grown in more than 100 nations worldwide, the sweet orange is one of the most economically significant and widely grown fruit crops in the world. In the United States alone, the citrus industry is worth $20 billion annually. The citrus industry is under attack by several, highly contagious plant pathogens, particularly citrus greening, or Huanglongbing, which debilitate the trees and threaten the future viability of citrus production in Florida, as well as many other growing regions worldwide. This threat has stimulated very significant investment of grower dollars in research to seek solutions.

“The immediate availability of these annotated assemblies will enable breeders to mine the database for genes associated with key agricultural traits, such as disease-resistance, temperature tolerance, fruit quality, and yield,” explained Fred Gmitter, Chair of the International Citrus Genomics Consortium and a citrus geneticist and breeder at the University of Florida. “In addition, they will enable research to understand the interaction of the host plant with the pathogen to develop disease mitigation strategies.”

In order to assess the quality of the assembly and refine genome annotation, the researchers also used 454 Sequencing Systems to analyze 16 transcriptome samples isolated from sweet orange seedlings which were subject to different environmental stressors, such as infection by pathogens and temperature extremes. “The resulting de novo transcriptome assembly proved to be extremely useful for gene prediction, allowing accurate reconstruction of full-length gene models and alternative spliced transcripts,” said Gmitter. “Mapping the transcript sequence reads from the different conditions to the draft genome assembly will be critical for inferring the pattern of gene expression in sweet orange in response to these different stressors, which were selected due to their relevance to plant breeders seeking to address industry needs.”

The sweet orange joins the growing list of plant genomes sequenced using next-generation 454 Sequencing Systems. Throughout just the last year, international research teams announced the draft sequences of the apple, cassava, soybean, wheat, wild strawberry, and cacao genomes, representing some of the most economically important crops for global food supply.

Do you wish to know more?

Tuesday, January 4, 2011

Bio Saga - 2010 in review


The stats helper monkeys at WordPress.com mulled over how Bio Saga Blog did in 2010, and here’s a high level summary of its overall blog health:
Healthy blog!
The Blog-Health-o-Meter™ reads Fresher than ever.

Crunchy numbers

Featured image
A helper monkey made this abstract painting, inspired by your stats.
A Boeing 747-400 passenger jet can hold 416 passengers. This blog was viewed about 3,000 times in 2010. That’s about 7 full 747s.
In 2010, there were 150 new posts, growing the total archive of this blog to 758 posts.
The busiest day of the year was June 8th with41 views. The most popular post that day was Computational Biologist @ Pfizer UK.


Where did they come from?

The top referring sites in 2010 were google.co.inen.wordpress.com,emperan.comobama-scandal-exposed.co.cc, anden.search.wordpress.com.
Some visitors came searching, mostly for list of pharma companies in noidabioinformatics tools and softwaresketan patel pfizerh1n1 vaccine serum institute, and campus interviews 2010 in apticraft.

Attractions in 2010

These are the posts and pages that got the most views in 2010.

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Python Text Processing with NTLK 2.0 Cookbook - Ebook Free Download

Python Text Processing with NTLK 2.0 Cookbook - Ebook Free Download

Life Science and Informatics

What is this?
is this a new industry?
or a old wine in a new bottle?

Well Life Sciences and Informatics can be anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining, database creation, in the area of biology, chemistry , bio-chem space.

There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies in this sphere.

now how good are these companies doing?
how good are they in terms of the international markets and how profitable is their business?
what do they do?
their clients?

These are some interesting things that could be discussed in this blog page...

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