RGITBT Biotechnology, Pune

RNA-Seq Data Analysis Online Course

2011-11-21T12:26:00.000+05:30

Making Sense of RNA-Seq Data

RNA-Seq is sequencing of steady state RNA in a given sample.RNA-Seq is used for 1. identifying allele specific gene expression 2. finding novel transcripts and isoforms and 3. differential gene expression. This training programme exposes participants to the available public domain tools and techniques for the analysis of RNA-Seq data and addresses complete analysis pipeline from mapping reads to differential expression and systems biology. Course delivery includes prerecorded webinars and the exercise labs.

Course Duration

Course will run for four weeks from 02.01.2012 to 29.01.2012.

Course Material

Course material will be delivered online for each week at the start of the week. Register at http://www.labindia-gpod.com or write to uday@labindia-gpod.com

Registration

Send a copy of your biodata along with DD of Rs 5000/- in the name of Labindia Instruments Pvt. Ltd. payable at Thane to Co-ordinator, Labindia-GPOD, Swnand, Jivan Vihar Housing Society, SB Road, Pune or make online payment with debit/credit card using payment gateway.

1. Tools for mapping reads to reference genome or transcriptome

A. Webinar : Overview of available tools and techniques for mapping reads to reference genome

B. Lab Exercises: Mapping reads to reference genome using Bowtie

2. De novo assembly of Transcriptome

A. Webinar : Tools and algorithms for De novo transcriptome assembly

B. Lab exercise : Using MIRA for De novo assembly

3. Finding isoforms and novel transcripts

A. Webinar : Overview of tools available for finding novel transcripts and isoforms

B. Lab exercises: Use of TopHat and Cufflink for finding isoforms and novel transcripts

4. Summarising mapped reads

A. Webinar : Review of tools for summarising mapped data and performing QC

B. Lab exercises : R Bioconductor tools for summarising mapped reads and QC

5.Normalization and Differential Expression

A. Webinar : Review of tools and method for normalising and analysis of differential expression of RNA-Seq data

B. R and Bioconductor tools for differential expression analysis prefernce will be given to DESeq package.

6. Gene set and pathway enrichment

A. Webinar : Overview of tools for gene set and pathways enrichment

B. Lab exercises : Goseq, Gostat and DAVID tools for enrichment analysis of differentially expressed genes.

8th BioSpectrum-ABLE study of Indian BioTech Industry 2010

2010-07-01T18:21:00.000+05:30

Press Release - June 17, 2010
Indian biotech industry grows 17% to touch USD 3 billion mark: 8th BioSpectrum-ABLE study
3 companies from Delhi NCR--Panacea, Jubilant, Eli Lily--in top 20 biotech companies list; West and South Biocluster dominate

New Delhi June 21, 2010 - The Indian biotech industry has grown 3-fold in just 5 years to report revenues of US $3 billion in 2009-10, a growth of 17% over the previous year.With revenues of Rs 6631 crore, the Western Biocluster emerged as the biggest contributor to India’s Biotech sector revenues followed by the Southern Biocluster contributing Rs. 5538 crore.
Western India continued to dominate India’s biotech industry with 46% share in the overall revenues of Rs. 14,199 crore from 137 companies in the region.

Gujarat state contributed about 8% of the total revenues at Rs. 1100 crore, by registering a growth of about 50%. Pune’s contribution went down as Serum Institute of India suffered contract set backs. West is home to top Bioagri companies such as Monsanto, Mahyco and Ajeet Seeds and MNCs like GlaxoSmithKline, Roche, Aventis Pharma, Wyeth, Quintiles. Four of India’s top 10 services companies (CROs) are also based out of West, including the No 1 CRO in the Indian industry – Quintiles India (Rs 375 crore).

The Northern Biocluster contributed just about one-seventh of the revenues at Rs. 2030 crore. India’s National Capital Region (NCR), home to the Top 3 companies, Panacea (Rs. 703 crore), Jubilant (Rs. 249 crore) and Eli Lily

(Rs. 187 crore), contributed 56% of the revenues from North. This cluster is better known for its research institutes and of course, government bodies. (see para below). Of the three large companies in the North, Panacea is the only one that grew at 17.86%, a growth rate higher than the industry growth rate.

According to the ABLE-BioSpectrum survey South continues to remain India’s largest Biotech cluster in terms of the number of companies adding 9 new biotech companies, highest in the country during the year. The region has 172 biotech companies (compared to 137 companies in the West) which posted revenues of Rs 5537.68 crore during the year making up 39% of the overall revenues. Eastern India does not add any significant revenues to the country’s overall BioTech pie.

Bangalore-based biopharmaceuticals firm Biocon, known for insulin and cancer drugs topped the BioSpectrum-ABLE list of Top 20 Biotech Companies after a gap of four years growing at 29.34% to record revenues of Rs. 1180 crore.

Hyderabad based Nuziveedu Seeds Limited (NSL), the largest hybrid seed company in India, sold nearly 7 million packets of Bt cotton seeds in 2009-10 giving it a market share of 36% as also the number one supplier of rice seeds status in the private sector. Nuziveedu emerged as the 4th largest BioTech company in India.
This has been revealed in the 8th annual survey conducted jointly by the Association of Biotechnology Led Enterprises (ABLE) and monthly journal, BioSpectrum, from the CyberMedia group based on inputs from over 150 biotech companies.

The Biopharma sector contributed nearly three-fifth to industry’s revenues at Rs. 8829 crore a growth of 12% followed by Bioservices at Rs 2639 crore and Bioagri at Rs. 1936 crore. The remaining revenue came from the Bioindustrials segment with a contribution of Rs 564 crore and Bioinformatics at Rs 231 crore.

NCR clusters’ focus on research institutes is visible among many others in the form of a development of a 200 acre Health Biotech Science Cluster (HBSC) at Faridabad. A multidisciplinary approach to education and research, this Biotech cluster would comprise Translational Health Science & Technology Institute (THSTI), Regional Center for Biotechnology (RCB) Center for Vaccinology, Molecular Medicine Center, Center for Diagnostics, Biotech Park, Center for Health Science Technology, Center for Platform Technologies, UNESCO Center, Incubator and a Center for Animal Model for Clinical Advances.
As a first step, a temporary THSTI lab was recently inaugurated at Gurgaon. This would be shifted to the main site at Faridabad in the next three years after the infrastructure is ready.
Besides, there is the biotech park at Lucknow offering a very good platform for the small and medium biotech companies to do research, collaborate and expand their business. The Biotech Parks at three locations —Sitapura-Jaipur and Chopanki, Bhiwadi (Alwar), and Borandi, Rajasthan have been initiated by Rajasthan State industrial Development & Investment Corporation (RIICO).

It is proposed to set up a biocluster at Mohali (Punjab), a biotech park at Chandigarh and another one at Nalagarh in Himachal Pradesh-- to provide the much needed boost to the biotech companies in the North region.

The sunrise sector earns a little more than half its revenue from exports.

Biopharma and Bioservices sector contributed 63% and 33% to the total biotech exports respectively. The Bioagriculture, Bioindustrial and Bioinformatics Sectors remained focused on domestic operations bringing in nearly 90% of their revenues from India.

The BioSpectrum study notes that the biotechnology ecosystem has become strong with technology providers and the biotech education sectors playing a key role.

“Overall, there is cautious optimism within the biotech industry and the recent government efforts to boost the infrastructure and support for various industry initiatives will bring succour for the industry,” says Narayanan Suresh, Group Editor of BisoSpectrum.

Biocon, Serum Institute Top Biotech Companies
Bangalore-based biopharmaceuticals firm Biocon, known for insulin and cancer drugs had the highest revenue in 2009-10. It topped the BioSpectrum-ABLE list of Top 20 Biotech Companies after a gap of four years growing at 29.34% to record revenues of Rs. 1180 crore.

Pune-based Serum Institute of India, that makes one out of every two vaccines produced in the world, slipped to No. 2 position with revenues of Rs. 850 crore. Last year, Serum was the first company in India approached by the World Health Organization to develop and manufacture the H1N1 vaccine to fight the swine flu pandemic.

Panacea Biotec, Nuziveedu Seeds and Reliance Life Sciences were ranked No 3, 4 and 5 respectively
The New Delhi headquartered pharmaceuticals, biopharmaceuticals and vaccine maker, Panacea Biotech, played a key role in eradicating polio by supplying over six billion doses of oral polio vaccine to the Government of India and UNICEF.

Nuziveedu Seeds Limited (NSL), the largest hybrid seed company in India, sold nearly 7 million packets of Bt cotton seeds in 2009-10 giving it a market share of 36% as also the number one supplier of rice seeds status in the private sector.

Reliance Life Sciences, earned 70% of its topline growth from biopharmaceuticals. The company has set up the first cord blood repository in South Asia and offers cord blood banking services to public.

The next 5 positions went to Quintiles, Rasi Seeds, NovoNordisk, Shantha Biotech and Mahyco.

According to the ABLE-BioSpectrum survey South continues to remain India’s largest Biotech cluster in terms of the number of companies adding 9 new biotech companies, highest in the country during the year. The region has 172 biotech companies (compared to 137 companies in the West) which posted revenues of Rs 5537.68 crore during the year making up 39% of the overall revenues.
Source: 8th BioSpectrum-ABLE study of Indian BioTech Industry 2010.

Future growth pegged around 20%

The BioSpectrum-ABLE study is not optimistic about the industry going back to the days of heady growth of 30% or more as most industry leaders agree that the industry is maturing and an annual growth will be around 20% in the near future.

The BioServices sector is now moving towards becoming regional players with many companies expanding their footprint to South East Asian countries.

The study points out that even though the moratorium on Bt brinjal and the uncertainty over regulatory approval for genetically-modified (GM) foods has not had much impact on the BioAgri industry’s performance, the industry is waiting for the correct signals from the regulator. The recent regulatory approval to conduct field trials of 17 crops has sent out mixed signals about the future prospects of the sector.

Also, the added public scrutiny over GM products due to the relentless campaign against Bt brinjal has added to the misery of the Bioagri sector. There is now a clamor for further reduction in prices of Bt cotton with the demand to scrap the technology fee charged by the innovator.

Notes to the Editor:

Companies shared information with us to the extent it was possible by them about their companies and the industry.

The revenues considered for the analysis are biotech products sales and service figures. In several cases, where revenue figures were not available estimates were arrived talking to industry experts.

This year in the list of Top 20 biotech companies, services companies in the drug discovery space have been taken into account, while diagnostics companies have not been considered.

Biotech suppliers’ revenues are not considered as part of the biotech definition.

Biopharma included products made by fermentation/animal cell culture (not animal extracts) and plant cell culture (not plant extracts).

The Bioagri segment analysis has included only the GM seeds and molecular markers and related products. So, the hybrid seeds business is not a part of the agri-business sales values.

For all the ranking purposes, we have taken the biotech business only into consideration.

Wherever turnover is mentioned it means, sales turnover from biotech. Therefore, turnover wherever mentioned is not necessarily the total sales turnover of the company.

About BioSpectrum

BioSpectrum and BioSpectrum Asia offer an integrated B2B media platform for life sciences industry in India and the Asia Pacific region. Together they offer an online portal, fortnightly digital magazine and monthly print magazine as formats of delivery. The BioSpectrum was awarded for Excellence in New Business Models Category at the Asian Publishing Award 2008.

About CyberMedia

CyberMedia is the largest specialty media house in South Asia. It has leading media brands in the region including Dataquest, PCQuest, Voice&Data, BioSpectrum, BioSpectrum Asia, DARE, Global Services, Living Digital, MIT’s Technology Review and Halsbury’s Law Monthly

CyberMedia reaches out to a community of over 1.5 million people through publications, websites, events and TV programs. Its brands cover infotech, telecom, biotech, entrepreneurship, outsourcing, consumer electronics, and legal domains.

Its media services include IDC India, the leading ICT market research company in the region; and Content Matrix, USA which provides through its subsidiaries, custom publishing and content management services.Or www.cybermedia.co.in

2010-06-16T17:04:00.001+05:30

Rajiv Gandhi Institute of IT and Biotechnology, Bharti Vidyapeeth Deemed University, Pune-411046, India

Program

M. Sc. Bioinformatics is a two year four semester program. Program has been designed in such a way that students can handle, analyze and interpret the biological data generated through the empirical biology using advanced technologies such as genome sequencing, microarray, proteomics, and epigenetics to name the few. Bioinformatics being interdisciplinary field, the program flow has been characteristically laid from foundation courses to professional and industrial modules through the core and advanced modules. The entire curriculum is distributed over five levels to perfectly train students for corporate readiness. The levels are respectively, Foundation, Core, Advanced, Project and Industry Seminars.

Eligibility for M.Sc Bioinformatics:

A student who has obtained Bachelor’s degree with minimum 50% in (i) B.Sc. (Biotechnology / Microbiology / Biochemistry / Zoology / Botany /Agri/ Chemistry /Mathematics /Statistics / Computer Science). (ii)B. Pharm (iii). MBBS (iv) BDS (v) BAMS (vi) BHMS (vii) B.E. in Computer Science or Information technology or Biomedical Engineering will be considered eligible for admission to M.Sc Bioinformatics course.

Course Fee

Rs 50,000/- per semester including wet lab and tuition fees. For Foreign Students fees is US $ 6000 for two years.

Contact Address

Principal,
Rajiv Gandhi Institute of IT and Biotechnology,
Bharati Vidyapeeth Deemed University Campus,
Pune Satara Road, Katraj,
Pune 411046
Phone 020-24379013, 24365713
uday.deshpande@bharatividyapeeth.edu

Do send a copy of your inquiry to uddeshpande@yahoo.com

Biotech Training Program

2010-05-29T14:16:00.000+05:30

Labindia Lifesciences in collaboration with Rajiv Gandhi Institute of Information Technology and Biotechnology, Bharati Vidyapeeth University, Pune (RGITBT)have created state of the art advanced laboratory infrastructure to impart high end training in emerging areas of biotechnology like genomics and proteomics.

Advanced Innovative Short term training Programs (AISP) are not routine training programs but are advanced and innovative one to provide exposure to advanced technologies. These programs have been designed to impart expertise to the participants by industry and academia experts. A student will get hands on training on

specific subjects or domains. Currently we are offering 10 days training program.

Date-7th June 2010 to 16th June 2010. Venue- RGITBT,Bharti Vidyapeeth,Pune.

Program Structure-

The training program shall include five modules namely Animal Cell Culture, Basic PCR,

Real Time PCR, Advanced optical Microscopy, Basic and applied Bioinformatics.

All the participants will be awarded certificate of participation. The fees for the training program shall be Rs.20,000/- per participant for all modules covered under the program. The fees shall include course material, lunch, tea and snacks during the period of the training program. The training program has been designed in the modular fashion, participants shall be

allowed to select a specific module or modules as per their choice. The fees for the individual modules will be as indicated below:

1. Animal Tissue Culture Rs 5000

2. PCR Rs 4000

3. RT PCR Rs 12000

4. Advanced optical Microscopy Rs 6000

5. Basic and applied Bioinformatics Rs 3000

The fees shall include course material, lunch, tea and snacks the period of the training program.

Accommodation facility will be provided to outside candidates on request with extra charges.

FOR MORE DETAILS AND REGISTRATION CONTACT-

Dr.Prashant Khadke

Application Support Scientist

Applied Biosystems Divisin,Labindia Lifesciences.Mumbai.

Email- kprashantp1@gmail.com ,khadkepp@labindia.com

Cell- 96196 85840

Workshop on Advanced Microscopy

2010-03-04T15:05:00.000+05:30

Rajiv Gandhi Institute of IT and Biotechnology, Bharati Vidyapeeth University, Pune in collaboration with Labindia, Thane is organizing a three day workshop 0n “Optical Microscopy—Basic and Advanced”.

The details of the program are given in the attached brochure. You are requested to circulate this amongst your colleagues. As the number of participants will be limited to 15, you are requested to confirm your registration at the earliest by sending mail to Dr. Uday Deshpande at mailID : uday.deshpande@bharatividyapeeth.edu.
Participants are allowed to bring their material for the image analysis.

Uday Deshpande,
Professor in Biotechnology,
Rajiv Gandhi Institute of IT and Biotechnology,
Bharati Vidyapeeth,
Katraj,
Pune- 411046
9970827533
uday.deshpande@bharatividyapeeth.edu
uddeshpande@yahoo.com

New Affiliation

2009-12-05T07:58:00.001+05:30

Dear All,

I have joined Rajiv Gandhi Institute of Information technology and Biotechnology, Pune as a Professor in Biotechnology. You can approach me at my mail ID uddeshpande@yahoo.com. We will meet on this block more frequently with new topics for discussion.

Uday Deshpande

5 Personal Core Competencies for the 21st Century By Sean Silverthorne

2009-08-14T10:43:00.001+05:30

Every epoch requires people and organizations to develop core competencies or skills needed to be successful. In the time of Henry VIII (yes, I am watching The Tudors), key competencies to master probably included fealty to a powerful lord and skill with a rapier. Not so much in demand today, however. Read more at Bnet Blog

By Sean Silverthorne

Six secrets to success—how to build a sustainable biotech business

2009-06-05T12:43:00.002+05:30

What are the core elements of a successful biotech?

Francesco De Rubertis, Roman Fleck & Werner Lanthaler have discussed six success to secrets of successful biotech business in the article published in Bioentrepreneur. To read the complete story visit the link http://www.nature.com/bioent/index.html

Goldman Sach Report

2009-05-24T18:31:00.003+05:30

Ten things for India to achieve its 2050 potential, by Jim O'Neill and Tushar Poddar of Goldman Sach's have proposed 10 point agenda foreconomic policy reforms for India. It is difficult summarise the report but the poingt no. 4 "It also needs both to significantly raise its basic educational standards, and increase the quality and quantity of its universities." is worth to look at more seriously from the point of need for trained and skilled manpower. The report is available at http://www2.goldmansachs.com/ideas/brics/ten-things-doc.pdf.

Beyond borders: global biotechnology report 2009:Ernst & Young

2009-05-06T18:27:00.001+05:30

Global financial crisis making biotech business model unsustainable according to Ernst & Young

Deep financing challenges separate haves and have-nots and accelerate move to sustainable models

Boston, 5 May 2009 – Despite worldwide economic turmoil, the global biotechnology industry delivered a solid financial performance in 2008, according to Beyond borders: Global biotechnology report 2009, Ernst & Young’s 23rd annual report on the biotech industry. However, the prolonged and systemic funding drought is placing the business model that fueled biotech growth for the past 33 years under unprecedented strain.The report released today says that four sweeping, paradigm-shifting trends should lead to new, more sustainable ways of funding drug development: a wave of generic drugs based on today’s top blockbusters, the expansion of personalized medicine, fundamental healthcare reform in the United States, and the continued globalization of the industry.

“This is not business as usual for the biotech industry,” said Glen Giovannetti, Ernst & Young’s Global Biotechnology Leader. “Unlike prior funding droughts, this crisis is systemic, deep and protracted. To thrive in this environment, firms will need to bring the creativity that has long been the industry’s hallmark to establishing more durable models for funding innovation.”

Key financial results:

Revenues of publicly traded biotechs grew 12% to US$89.7 billion in 2008. The global industry’s net loss improved 53%, from US$3 billion in 2007 to US$1.4 billion in 2008. The US industry reached aggregate profitability for the first time.
Capital raised declined sharply in 2008. Companies in the Americas and Europe raised US$16 billion in 2008, a 46% decline from 2007. IPO funding fell 95% to US$116 million.
Biotech venture financing remained relatively strong, falling only 19% from 2007’s all-time record to about US$6 billion in 2008.
Industry deal making remained brisk. The total value of M&As involving US biotechs reached more than US$28.5 billion — a record high when adjusting for megadeals that took place in prior years. In Europe, M&A transactions totaled US$5 billion.

“Like firms in most markets, European biotechs were clearly impacted by the financial crisis,” said Jürg Zürcher, Ernst & Young’s Biotechnology Leader for Europe, Middle East, India and Africa. “Many are scrambling to raise capital, restructure operations and use deals creatively to survive. Consolidation seems inevitable.”

New pathways to sustainability

The challenge for the industry, according to Beyond borders, is turning an existential threat into a Darwinian opportunity. The potential solution lies in four paradigm-shifting trends that promise to accelerate the transition to sustainable business models:

Generics: Generics based on today’s top blockbusters should loosen governments’ and insurers’ budgetary constraints and mitigate pricing pressures on innovative drugs, permitting better margins.

US healthcare reform: The potential shift toward universal healthcare coverage in the world’s largest drug market will likely incorporate pay-for-performance in reimbursement decisions. Incentives for true innovation should help biotechs sustain returns.

Personalized medicine: Personalized medicine will increase the relative value of research and early development — biotech’s traditional strengths — giving biotechs more bargaining power and better valuations. Meanwhile, more efficient drug development will lower R&D costs, making it easier for firms to make the journey to self-sufficiency.

Globalization: Growing strengths in emerging markets will facilitate creative solutions — from new “win-win” ways of allocating increasingly valuable ex-US rights to creative alliances and new sources of capital. Meanwhile, Asian business models could provide solutions for struggling Western firms.

“But these trends will also bring new market pressures — from a higher bar on reimbursement to new sources of competition. “To seize the opportunities in these four drivers, companies need to be proactive,” says Giovannetti. “Firms should understand how these trends impact them, prepare for them, and where possible, help shape them.”

Key regional findings

United States

Revenues of US public biotechs grew by 8.4% in 2008, down from 11.3% in 2007.
The US publicly traded industry posted an aggregate net profit for the first time — US$0.4 billion.
Despite the crisis, venture capital raised in the US reached US$4.4 billion in 2008 — the second-highest total in history, behind only the record US$5.5 billion raised in 2007.

Europe

Revenues of European public biotechs increased 17% to €11.2 billion.
Capital raised by European biotechs fell from €5.5 billion in 2007 to less than €2 billion in 2008.

Asia-Pacific

Asia-Pacific biotech revenues grew by 25% in 2008, led by strong growth in Australia.
In Australia, public-equity funding fell to levels not seen since 2002. There were a handful of IPOs in Japan and China and strong private-equity funding growth in India.

Biotechnology Management

2009-04-04T13:05:00.001+05:30

India is emerging as destination for biotech development requirement of global companies. Economic Times, 23rd Nov., 2008.

Is that true ? Whats happening to biotech industry at the global level especially in the troubled economy . News is that US biotech industry sector is suffering. Small and medium units are on run away money while large ones are holding their resources with no new recruitment.

How is Indian Biotech industry performing these days ? Biotech sector in India was growing at the speed of 35% for the last five years. Growth slumped to 20% in the fiscal year 2007-2008 and 2009. The sector is expected to touch US$ 5.00 billion mark by 2010.

This prediction could stand true as DBT, Govt of India has taken specific steps to promote this sector. Such as providing angel finance through various schemes, launch of biotech parks in various parts of the country and providing single window systems for govt clearances. The Patenting scenario has also been improving in the country. This naturally will boost the biotech sectors growth.

The most important need of the biotech sector is appropriately trained manpower. Is it available in the country?. The wave of biotech has created spawn of the institutions imparting biotech education but with inadequate facilities. Large number of the graduates (B.Sc. and B.Tech) are being pushed in to market. The training skills imparted to them are so week that they do not find right job opportunities.

There is also no correspondence between the number of biotech graduates qualifying to the number of seats available to join the post graduate programs in biotechnology. There are very few institutions in the country that have adequate facilities to conduct the biotech programs.

This forum will discuss the current issues in biotechnology at education, research and management fronts. Forum also will post information on select post graduate programs in biotechnology.

Comments and Suggestions are most welcome.