Briefings in Bioinformatics Advance Access published August 12, 2010B RIEFINGS IN BIOINF ORMATICS . page 1 of 10 doi:10.1093/bib/bbq027Bioinformatics education in IndiaUrmila Kulkarni-Kale, Sangeeta Sawant and Vishwas ChavanSubmitted: 10th May 2010; Received (in revised form): 29th June 2010AbstractAn account of bioinformatics education in India is presented along with future prospects. Establishment of BTIS net-work by Department of Biotechnology (DBT), Government of India in the 1980s had been a systematic effort inthe development of bioinformatics infrastructure in India to provide services to scientific community. Advances inthe field of bioinformatics underpinned the need for well-trained professionals with skills in information technology Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010and biotechnology. As a result, programmes for capacity building in terms of human resource development wereinitiated. Educational programmes gradually evolved from the organisation of short-term workshops to the institu-tion of formal diploma/degree programmes. A case study of the Master’s degree course offered at theBioinformatics Centre, University of Pune is discussed. Currently, many universities and institutes are offering bio-informatics courses at different levels with variations in the course contents and degree of detailing. BioInformaticsNational Certification (BINC) examination initiated in 2005 by DBT provides a common yardstick to assess theknowledge and skill sets of students passing out of various institutions. The potential for broadening the scope ofbioinformatics to transform it into a data intensive discovery discipline is discussed. This necessitates introductionof amendments in the existing curricula to accommodate the upcoming developments.Keywords: bioinformatics; education; syllabus; computational infrastructure; certification; biotechnologyinformation system; IndiaINTRODUCTION Ramachandran plot that provided the foundationThe beginning of the era of bioinformatics is marked of modern structural biology/bioinformatics . Asby early studies such as the compilation and analysis a consequence of these and other discoveries, bio-of large sets of protein sequences by Late Dr informatics has grown into a full-fledged scientificMargaret Dayhoff to study molecular evolution in discipline of knowledge discovery. It has becomethe 1960s . These efforts led to the development an essential and integral component of frontline re-of one of the earliest databases in the area of bio- search in life sciences. The problems addressed usinglogical macromolecules—Protein Information bioinformatics range from simple analyses of singleResource, popularly known as PIR database. This gene/protein data to modelling of complex data suchwas followed by the development of computer pro- as systems biology. Bioinformatics employs the prin-grammes, often written by the scientists themselves, ciples of statistics, mathematics, physics and chemistryfor the application of quantitative methods to study to address the problems in biology by using compu-biological data. History of bioinformatics in India tational methodologies.dates back to the 1960s when Prof. G. N. The early contributors to the field of bioinformat-Ramachandran and colleagues derived the famous ics were from either life sciences or physical sciencesCorresponding author. Vishwas Chavan. Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK 2100,Copenhagen, Denmark. Tel: þ45 35 32 14 75; Fax: þ45 35 32 14 80; E-mail: firstname.lastname@example.orgDr Urmila Kulkarni-Kale, Director, Bioinformatics Centre, University of Pune has been teaching wide range of courses inBioinformatics for 18 years, designed syllabi and been faculty at national and international workshops. Her research interests includeviral comparative genomics, immunoinformatics and Bioinformatics.Dr Sangeeta Sawant is teaching courses in varied areas of Bioinformatics at University of Pune for 16 years and has designed syllabifor various courses. Her research interests include structural bioinformatics, molecular modeling and simulations to study protein/peptide structures and functions.Dr Vishwas Chavan is at the Secretariat of the Global Biodiversity Information Facility (GBIF), with 19 years experience inbiodiversity and ecosystem informatics. His recent interest is to develop ‘data publishing framework’ that address social, politicaland cultural issues responsible for expediting discovery and publishing of biodiversity data (http://www.vishwaschavan.com/).ß The Author 2010. Published by Oxford University Press. For Permissions, please email: email@example.com
page 2 of 10 Kulkarni-Kale et al.who had realized the potential of computational of life science researchers in the application ofapproaches in the study of biology. As the discipline bioinformatics. This has successfully ushered inevolved and its scope became broader, the demand a new paradigm in India, through integrationfor trained human resource started growing. This of bioinformatics approach with experimentalnecessitated the establishment of formal training pro- research.grammes. Initially, a few research institutes intro-duced short training programmes of a few days tofew weeks in duration. The topics covered in these BIOINFORMATICS EDUCATIONprogrammes varied from introduction to the field ofbioinformatics to specialized themes like biological IN INDIA: EVOLUTION &databases, algorithms and applications of bioinfor- CURRENT STATUS The centres under the BTIS network, right Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010matics. Formal long-term courses were subsequently from their inception, have been carrying out gener-launched by many universities/institutes world alized as well as special theme-based short-termover [3–8]. training programmes in different areas of bioinfor- matics. The training programmes in the 1980s focused on building awareness of bioinformaticsGROWTH OF BIOINFORMATICS among biologists, medical practitioners, statisticians,IN INDIA mathematicians and IT professionals. These wereFormalization of bioinformatics activities in India followed by detailed workshops on topics like bio-began in the early 1980s with the establishment of logical databases, database searches, algorithms for se-a nation-wide network of Distributed Information quence analysis and their applications, phylogeneticCenters (DICs) under the umbrella of the analysis, structural bioinformatics, molecular model-Biotechnology Information System (BTIS), by the ling and simulations etc. These activities proved to beDepartment of Biotechnology (DBT), Government extremely useful to a variety of user groups like re-of India (http://www.dbtindia.nic.in/; http://www searchers, academicians and industry professionals..btisnet.gov.in/index.asp) [9, 10]. These centres were The short-term training activities are now well coor-assigned the mandate to (i) carry out research in dinated across the BTIS network with DBT publish-specialized areas and (ii) provide bioinformatics sup- ing an annual training calendar (http://www.btisnetport and services to the scientific community at large. .gov.in/uniquepage.asp?ID_PK¼21).The BTIS network today includes six Centers of In the 1990s, application of novel, high-Excellence (CoEs), 10 DICs, 51 Sub-DICs and throughput technologies and automated procedures61 Bioinformatics Infrastructure Facilities (BIFs) in life sciences resulted in the generation of largecoordinated by the apex centre at DBT, New volumes of biological data across the omics series.Delhi (http://www.btisnet.gov.in/index.asp). The With the changing nature, volume and complexitygeographic distribution of the centres ensures easy of data (whole genome sequences, proteomics, struc-access of informatics infrastructure to maximum tural genomics, transcriptomics, metabolic and signalnumber of academic and R&D institutions in the transduction pathways, protein–protein interactions,country. The expansion of the network has also cul- etc.) specific and specialized technology became ne-minated in broadening expertise in various domains cessary for processing and analysis of the data.of bioinformatics, viz. structural bioinformatics, gen- Approaches based on application of artificial intelli-omics, proteomics, immunoinformatics, etc. gence methods, machine learning techniques, fuzzyResearchers from these centres have significantly logic, grid computing, parallel programming, etccontributed to the development of a variety of pri- were developed. With the changing scenario itmary and derived databases, a large number of became necessary to train students/professionals toalgorithms to analyse data at different levels of bio- be ‘bioinformaticians’. The field has been evolvingcomplexity and servers for prediction of various so rapidly that the training programmes should em-properties of biomacromolecules (http://btisnet power the students not only to learn and apply the.gov.in/writereaddata/12271108171_Publication_ core tools and techniques but also inculcate aList.pdf) . The BTIS network offers computing life-long learning ability that allows them to absorbfacilities as well as domain expertise, which and master new technologies/concepts as theyhave induced interest amongst a large number emerge.
Bioinformatics education in India page 3 of 10 The full-fledged formal training programmes in combination of computational and experimentalbioinformatics were therefore designed with the fol- components. A few of the ADB pass-outs alsolowing objectives. became entrepreneurs by establishing their own start-ups in the areas of bioinformatics, chemoinfor- To train students in the fundamental disciplines matics and medical informatics. relevant to bioinformatics Full-fledged Master’s degree programmes in bio- To help them acquire the essential IT and bio- informatics started later have either replaced the informatics skills ADB course or coexisted with it for a few years at To develop the competency in problem solving. the universities mentioned above. The students trained with these objectives are MSc programmes in bioinformatics Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010anticipated to meet the interests of stakeholders, Scientific and technological advances, viz. comple-viz. the funding agencies as facilitators, educational tion of full genome sequencing projects of importantinstitutes as prosumers and academia/RD labora- organisms including human, rise of omics series,tories/industry as employers. availability of high performance computing facilities, in the early years of the 21st century furtherAdvanced Diploma in Bioinformatics increased the demand for trained manpower.A 1-year Advanced Diploma course in This called for institution of a full-fledged 2-yearBioinformatics (ADB) was launched in 1997 in the Master’s degree course (MSc) in bioinformatics.five DICs viz., Jawaharlal Nehru University (JNU) The first MSc programme in bioinformatics was(New Delhi), University of Calcutta (Kolkata), started at the University of Pune in July 2002, withMadurai-Kamraj University (Madurai), Pondicherry financial support from the DBT (http://bioinfoUniversity (Puducherry) and University of Pune .ernet.in/). Subsequently, an MTech course in(Pune). It was designed for students who completed computational and systems biology was launched attheir Master’s degree in basic sciences or Bachelor’s JNU, New Delhi in 2006 and MSc in bioinformaticsdegree in medicine/engineering/pharmacy. The at Pondicherry University (Puducherry) in 2007. Asobjective of ADB was to create human resource a representative Master’s degree programme, a casein bioinformatics to satisfy the growing need in study of MSc Bioinformatics at the University ofvarious sectors. The ADB syllabus was designed to Pune is presented below.train students to achieve proficiency in the use of The MSc bioinformatics programme at theexisting tools as well as the development of University of Pune has earned a reputation as onenew tools. Indeed, the syllabus that was designed of the best in the country. The course has been de-for ADB in 1997 was in congruence with the signed to ensure a balanced and comprehensive‘dream’ syllabus proposed by Russ Altmann in training in bioinformatics as well as related subjects.1998 . The course consists of a total of 100 credits distrib- The ADB course had to address the needs of stu- uted over four semesters of 15 weeks each. A theorydents coming from different backgrounds. On one course of one credit is equivalent to 15 contact hoursside, students with formal training in biological sci- while a practical course of one credit requires 45 h ofences needed to learn mathematics, statistics and laboratory work. The weightages for theory, labora-computer science, whereas those from engineering/ tory courses and project work are 43, 37 and 20%,physical/chemical sciences required an in-depth ex- respectively. The learning process lays emphasis onposure to biology. Such a mixed composition of stu- hands-on experience and problem solving sessions.dents often proved to be an advantage as they The syllabus is designed to impart training not onlycomplemented each other in understanding the mul- in bioinformatics but also in biology, mathematics,tiple disciplines and significance of bioinformatics. statistics and information technology, which The ADB opened up opportunities for students to form the foundation of bioinformatics. Figure 1secure admission into the PhD programmes of (A and B) depicts the allocation of credits forreputed universities in India/abroad and jobs at vari- theory and laboratory components of these subjects,ous cadres ranging from technicians to scientists in respectively.academic institutions/industry. Several of these The courses in these subjects run through the fourassignments included research projects having semesters with increasing levels of complexity
page 4 of 10 Kulkarni-Kale et al. (Figure 2). Basic biology and mathematics form op- tional courses to students who studied mathematics and biology, respectively, in their Bachelor’s degree. Biological chemistry and genetic information flow and processing (molecular biology) are offered in the first semester while cell biology, genetics and experimental laboratory techniques are taught in the second semester. For specialized areas of bio- informatics, viz. immunoinformatics, parasite bio- informatics and metabolic pathway engineering, the corresponding areas of biology (immunology, para- Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010 sitology, metabolic pathways) are integrated with in- formatics. As depicted in Figure 2, statistics is taught in the first semester whereas advanced algorithms and techniques as applied to biological data mining are covered in the subsequent semesters along withFigure 1: Distribution of credits for the core subjectstaught in MSc Bioinformatics. (A) Percent credit alloca- pertinent topics in bioinformatics. Similarly, thetions for theory courses and (B) Percent credit alloca- courses imparting IT skills are introduced graduallytions for laboratory courses. The credits allocated for during the first to third semesters. The IT trainingproject work are not included in this distribution. includes various operating systems, programmingFigure 2: Semester-wise distribution of topics in the major disciplines in the syllabus of MSc bioinformatics atUniversity of Pune. Different colours as shown in tiles are used to indicate four semesters.
Bioinformatics education in India page 5 of 10languages (C, java and perl), database management Nationwide scenario of bioinformaticssystems and computer graphics and visualization. educationThe topics in bioinformatics are divided into Realizing the importance of bioinformatics as afour broad groups viz. databanks and sequence-based career opportunity for the young generation, manyapproaches, structural bioinformatics, genomics universities and institutions are now offeringproteomics, and biological data mining, which Diploma, Bachelor’s and Master’s level courses inare spread over the four semesters (Figure 2). India. Since it is not possible to provide comprehen-The course contents encompass biocomplexity sive overview of all of them here, some of the betterfrom macro to micro levels and vice versa. For ex- known ones are mentioned below. In addition to theample, there are modules in biodiversity informatics universities mentioned below, a few of those listed inon one hand and molecular phylogeny on the other, the Table 1 also offer Bachelor’s and Master’s degree Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010to enhance understanding at molecular level. courses in bioinformatics.Similarly, study of individual genes/proteins is fol-lowed by that of genomics and proteomics providing JNU, New Delhia perspective at the systems level. Chemoinformaticsis an important area of research and is included as a JNU introduced Advanced postgraduate Diplomaseparate course in the second semester. in Bioinformatics in 2000 at the Centre for The students get an exposure to research meth- Computational Biology and Bioinformatics, whichodologies in the project work during the fourth se- was later integrated into the School of Informationmester. Some of the projects carried out by the ADB Technology. In the year 2006, an MTech pro-and MSc students have led to publications in gramme in computational and systems biologypeer-reviewed journals [13–15]. replaced the Diploma course (http://ccbb.jnu.ac Rapid growth and developments in bioinformatics .in/education.html).call for revision of syllabus at regular intervals.Accordingly, the syllabus of MSc bioinformatics is Madurai Kamaraj University, Madurai.periodically revised at the Bioinformatics Centre,University of Pune. It compares well with the syllabi The Bioinformatics Centre, School ofof Master’s programmes offered at various universi- Biotechnology, Madurai Kamaraj University offeredties world over. A few differences feature due to a 1-year Advanced Diploma course in Bioinformaticsdegree of details and weightages allocated to found- during 1996–2006. The course was designed to pro-ing disciplines or areas of specialization. For example, vide an integrated outlook of biotechnology andbioinformatics programmes offered in the different bioinformatics (http://www.biotechmku.org/).universities/institutes in Germany are designed tofocus on the main research area of the parent uni- Pondicherry University, Puducherryversity/institute . The ADB and MSc programmes in bioinformatics The Bioinformatics Center of Pondicherryat the University of Pune turned out to be highly University currently offers MSc and PhDsought after professional courses leading to place- programmes besides modular courses in bioinfor-ments in academia as well as industry. To date, a matics (http://www.bicpu.edu.in/). Pondicherrytotal of 127 and 146 students have been trained in University, Madurai Kasmraj University and Annathe ADB and MSc (Bioinformatics) programmes, re- University (Chennai) are also due to start MSc inspectively. Of the 69% of the students, who have computational biology on a consortium basis fromsuccessfully completed these courses, 80% found the academic year 2010–11.placement in academia or industries in India andabroad. These budding bioinformaticians are contri- Indian Institutes of Technologybuting to a wide range of academic and commercialprojects not only in core scientific areas (drug Master’s level programmes in Bioengineering andand vaccine developments, clinical research, agrobio- Biotechnology offered by IITs include bioinformat-technology, etc.) but also in technological as- ics as core/elective courses.pects (software, database development and usersupport). Indian Institutes of Information Technology
page 6 of 10 Kulkarni-Kale et al. Indian Institutes of Information Technology Microbial Technology, Chandigarh; Institute of(IIITs), Allahabad offers MTech in Information Genomics and Integrative Biology, New Delhi,Technology with specialization in bioinformatics etc.). These programmes are mainly funded by the(http://bi.iiita.ac.in/index.html) whereas IIIT DBT, Department of Science and TechnologyHyderabad offers MTech in bioinformatics as well (DST), Council for Scientific and Industrialas MS by research in bioinformatics (http://www Research (CSIR), Ministry of Communications .iiit.ac.in/academics/programmes/postgraduate/ Information Technology (MCIT), Indian Councilmtechbio). of Medical Research (ICMR), Indian Council of Agricultural Research (ICAR) and University Institute of Bioinformatics and Applied Grants Commission (UGC). Availability of doctoral Biotechnology, Bangalore programmes has provided an impetus to research in Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010 bioinformatics. A postgraduate course of 18-month duration(three semesters) in bioinformatics is conducted bythe Institute of Bioinformatics and Applied CHALLENGES ANDBiotechnology (IBAB), Bangalore, since 2002 OPPORTUNITIES(http://www.ibab.ac.in/prog_bioinformatics.html). Emergence of bioinformatics has ushered in new ex- citements in Life Science research and opened up DOEACC Society new vistas in the career paths [8, 11, 16, 17]. Computational infrastructure is a crucial component The DOEACC Society, an autonomous body of for generating the human resource with desired skillsthe Department of Information Technology, and competencies. Through the establishment ofMinistry of Communications Information BTIS Network, DBT has played and continues toTechnology, Government of India, is dedicated to play a significant role in this direction.education in IT in the non-formal sector. The soci- Bioinformatics being a multidisciplinary field,ety has designed bioinformatics courses at four dif- teaching programmes require experts from the coreferent levels, ranging from basic diploma (‘O’ level) domain (bioinformatics) as well as from the basicto MTech (‘C’ level). The courses are run at desig- areas of biology, mathematics, statistics, computernated centres of DOEACC (http://www.doeacc science and information technology. Only a handful.edu.in), e.g. a B-level programme, MSc (Tech) in of teachers with the necessary teaching and researchbioinformatics, at the West Bengal University of experience in the field of bioinformatics are currentlyTechnology (WBUT), Kolkata. available. In most of the universities, the limited number of in-house faculty makes it necessary toPhD programmes in bioinformatics invite experts from other institutions. With increas-Research work in the areas of computational biology ing numbers of courses all over the country, there isand data mining leading to the award of doctoral de- a growing demand for experts/teachers in this field.grees has been carried out in India since late 1960s. This opens up opportunities for the overseasUniversity of Pune was one of the first universities to bioinformaticians to return to India, facilitatinghave started a PhD programme in 1997 in bioinfor- brain gain.matics perse and the first degree was awarded in 2000.Currently, PhD programmes in bioinformatics and Teaching bioinformatics to studentscomputational biology are offered by several central, as a component of Master’s degreestate and private universities, Indian Institutes of programmes in other disciplinesTechnology (IITs) as well as research institutes (e.g. In view of the wide spread applications in life scienceIndian Institute of Science, Bangalore; National research, a few universities have included bioinfor-Centre for Biological sciences, Bangalore; Centre matics as a subject in the curricula of Master’s degreefor Cellular and Molecular Biology, Hyderabad; programmes in zoology, botany, microbiology, bio-Centre for DNA Fingerprinting and Diagnostics, chemistry, biotechnology and bioengineering.Hyderabad; National Institute of Pharmaceutical Students of these subjects are the potential usersEducation Research at Mohali and other locations; of bioinformatics and hence need to be trainedvarious National Institutes of Technology; Institute of in an ‘application-oriented’ manner. Bioinformatics
Bioinformatics education in India page 7 of 10training is adding value to some of the engineering this examination. The examination is novel andand management degree programmes as well. We unique in that it employs a three-tier system of test-envisage that bioinformatics training will soon be ing, viz. objective, short answer and computationalincorporated into the curricula of medical sciences laboratory based assessments.so that the medical fraternity would be adequately The objective and short answer components ofequipped to apply modern methods of molecular the examination include sections on biology, basicmedicine in clinical practice research in future. mathematics, statistics, physics, chemistry, informa-Based on our experience of teaching bioinformatics tion technology and bioinformatics. The skillsto a few students with background in pharmacy and assessed in the laboratory based examination are:our interactions with experts working in the area of (i) application of the existing bioinformatics tools,drug design, we believe that formal training in bio- (ii) ability to analyse and interpret data and (iii) com- Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010informatics would empower pharmacists with new petency in programming. A national committeetools approaches for the entire spectrum of appli- of experts has framed the syllabus for BINC exam-cation areas, viz. drug discovery, delivery and metab- ination, which is compatible with Master’s levelolism. Similar views on the inclusion of teaching programmes.bioinformatics in pharmacy curricula have been ex- Candidates, who qualify in all the three individualpressed by Thorn et al. . components of the examination, are awarded a cer- tificate. This certification is intended to serve as aNeed for modular courses benchmark to facilitate industries and other potentialProfessionals from different domains of life, physical employers in recruiting bioinformatics professionals.and computer sciences can effectively utilize bio- As a corollary to the BINC certification, fellowshipsinformatics resources for knowledge discovery. In are also awarded to the top 15 BINC qualified can-view of this, there is a growing interest to acquire didates to pursue PhD in Indian institutes and uni-the requisite skills through short term, tailor-made versities in the area of bioinformatics andmodular courses in bioinformatics. To cater to this computational biology. This examination is openrequirement, BTIS centres funded by DBT are orga- to students from other countries as well, for the pur-nizing theme-based short-term training programmes pose of certification only.(http://www.btisnet.gov.in/uniquepage.asp?ID_ BINC examinations were conducted five timesPK¼21). MCIT, Government of India has also taken during 2005–10. A total of 2374 candidates, fromthe initiative to identify and fund Centres of 27 states and union territories of India have appearedExcellence with a mandate to design and deliver for these examinations, of which, only 50 candidatesmodular courses of short duration for professionals have qualified for certification amounting to a success(http://mit.gov.in/content/bio-informatics). rate of 2.1% (Table 1). While candidates fromPondicherry University and IBAB, Bangalore have more than 150 universities/institutes appeared forrecently launched such courses. the examinations, those who qualified came from only 18 of them. However, the representationBioInformatics National Certification of universities/institutes to which successful candi-Examination dates belong is becoming wider every yearRecent years have witnessed a mushrooming of bio- (Table 1). Of the candidates who qualified for certi-informatics training programmes in Indian universi- fication, 80% had formal training in bioinformaticsties and institutions, both from the public and private reflecting that these candidates had a distinct advan-sectors, with a wide variation in the course contents, tage over those who had limited exposure to bio-training period and methodology of training. In view informatics during their education or throughof this, recognizing the need to define the minimum self-study. Among the BINC certified candidatescore competency of the trained manpower in this the proportion of those with Master’s degree isarea, DBT has instituted the BioInformatics 88%, which is significantly higher than those withNational Certification (BINC) examination in 2005 a Bachelor’s degree (12%). This underlines the im-with the objective to certify the bioinformatics portance of education in basic sciences at Bachelor’sknowledge and skills of the students (http:// level as a prerequisite for adequate and comprehen-bioinfo.ernet.in/binc). However, formal training sive training in bioinformatics at the Master’s level.in bioinformatics is not a prerequisite to appear for Thus, the recent rush to introduce courses in
page 8 of 10 Kulkarni-Kale et al.bioinformatics at the Bachelor’s degree level by sev- mining and are expected to have a far-reachingeral institutes/universities appears to be premature impact on bioinformatics research. Furthermore,and ill-conceived since students do not get an op- new approaches are needed for cross-scale andportunity to have a sound foundation in basic sci- cross-discipline integration of data from biodiversityences. Similar views have been expressed by Natesh informatics, ecoinformatics and enviroinformatics,and Bhan  on the Bachelor’s degree programmes which is critical to a wide range of scientific andin biotechnology. educational purposes as well as for decision-making in the sustainable use of natural resources . TheseWay forward emerging trends, which would widen the scope ofThe resources available for bioinformatics education- bioinformatics, need to be incorporated in the curri-al programmes have been enriched over the period cula. For example, studies of interactions at levels Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010of last 10–12 years. The easy and efficient access to beyond molecular, such as cell–cell, species–speciesscientific knowledge through specialized journals, and species–environment as outlined in phylody-e-learning material, international conferences, work- namics studies  should find a place in the curri-shops, etc. has further augmented the development cula. Mathematical modelling and simulations ofof these programmes. The time is now ripe to an- these interactions should constitute an importantticipate a perceptible impact of the educational pro- component of bioinformatics training in future.grammes on research and developments in life The students should also be exposed to skills in sci-sciences in general and bioinformatics in particular entific writing and presentation, knowledge of intel-in the country. lectual property rights, ethics, morals and The first decade of the 21st century has witnessed socio-scientific attitude to ensure their overall devel-an unprecedented accumulation of biological data opment. We believe that with the inclusion of thesedue to spatio-temporal studies involving technolo- aspects in bioinformatics education, bioinformatics asgies that allowed capturing data at mega- and a discipline will move into ‘the Forth Paradigm’,milli-scales. The complexities and volume of result- facilitating data-intensive discoveries in biologicalant data posed new challenges for management and sciences . A recent survey carried out by theTable 1: University-wise distribution of candidates who qualified in BINC examinations (2005^10)Sr. No. Year Name of the University BINC Qualified Candidates1. 2005 çç- 02. 2007 Indian Institute of Technology, Kharagpur 1 Mohanlal Sukhadia University, Udaipur 1 University of Agricultural Sciences, Bangalore 1 University of Pune, Pune 4 West Bengal University of Technology, Kolkata 13. 2008 Institute of Bioinformatics and Applied Biotechnology, Bangalore 2 Jaypee Institute of Information Technology, Noida 1 Manipal Institute of Technology, Manipal 1 University of Pune, Pune 6 Vellore Institute of Technology, Vellore 24. 2009 Chaudhary Charan Singh University, Meerut 1 Indian Institute of Technology, Bombay 1 Indian Institute of Technology, Kanpur 1 International Institute of Information Technology, Hyderabad 1 JNU, New Delhi 1 Panjab University, Chandigarh 1 Patna University, Patna 1 Sardar Patel University, Gujrat 1 Sastra University, Thanjavur 1 University of Pune, Pune 20 Vellore Institute of Technology, Vellore 15. 2010 çç- 0 Total 50
Bioinformatics education in India page 9 of 10journal Nature clearly brings out the need for trained The help extended by Ms. Sunita Jagtap in data compilation isbioinformaticians as well as application of latest tech- greatly appreciated. V.C. acknowledges the Global Biodiversity Information Facility.nology of cloud computing for archival and proces-sing of genomic data to maximize the discoveriesbased on genomic data . FUNDING Department of Biotechnology, Government of India towards infrastructural facility and teaching programsCONCLUSIONS (ADB, M.Sc., CoE and BINC) at the BioinformaticsRecognizing the potential of bioinformatics, India Centre, University of Pune. Ministry of Com-has taken the early steps to establish the necessary munications and Information Technology, Govern-infrastructure and initiated the training programmes ment of India towards Center of Excellence in Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010in this area. Efforts in this direction have resulted Bioinformatics.in perceivable growth of bioinformatics and biotech-nology in the country. Several research projectshave been funded and successfully completed,resulting in the development of bioinformatics Referencesresources and publications in international 1. Dayhoff M. Atlas of Protein Sequence and Structure. National Biomedical Research Foundation. Maryland, USA, 1965.journals of high impact factor (http://btisnet.gov 2. Ramachandran GN, Sasisekharan V. Conformation of poly-.in/writereaddata/12271108171_Publication_List peptides and proteins. Adv Protein Chem 1968;23:283–438..pdf ) . The HRD activity has also culminated 3. Counsell D. A review of bioinformatics education in thein the development of core competency. UK. Brief Bioinform 2003;4:7–21.Bioinformaticians placed at strategic positions in the 4. Ranganathan S. Bioinformatics education–perspectives andbiotechnology and software industries have signifi- challenges. PLoS Comput Biol 2005;1:e52.cantly contributed to the value chain to generate 5. Koch I, Fuellen G. A review of bioinformatics education inIPR as well as revenue. India, with its strengths in Germany. Brief Bioinform 2008;9:232–42.information technology, increasing investments in 6. Yang MQ, Niemierko A, Yang JY, et al. Promoting inter/ multidisciplinary education and research in bioinformatics,bioinformatics infrastructure and human resource de- systems biology and intelligent computing. IntJ Comput Biolvelopment, is poised to play a greater role in the Drug Des 2009;2:207–20.global landscape in future. 7. Yang JY, Yang MQ, Zhu MM, et al. Promoting synergistic research and education in genomics and bioinformatics. BMC Genomics 2008;9(Suppl 1):I1. 8. Ranganathan S. Towards a career in bioinformatics. BMC Key Points Bioinformatics 2009;10(Suppl 15):S1. Department of Biotechnology, Government of India has been 9. Ramachandran S, Kolaskar AS. Bioinformation systems in instrumental in promoting bioinformatics activities in India. India, computer handling and discrimination of data. In: A large number of universities/institutes offer bioinformatics Glaeser PS (ed). CODATA. Elsevier Science B.V. 1987; education in India. 394–9. The spsectrum of formal education in bioinformatics ranges from short-term courses to PhD programmes. 10. Arora JR. Biotechnology Information System. A national A majority of the courses are funded by various Governmental Bioinformatics network. In: Growth of Biotechnology in India- agencies. A tribute to Dr. S. Ramachandran. Narosa Publishing House, 1992;157–65. 11. Natesh S, Bhan MK. Biotechnology sector in India: strengths, limitations, remedies and outlook. Curr SciAcknowledgements 2009;97:157–69.U.K.K. and S.V.S. express their deep gratitude to Prof. A. S. 12. Altman RB. A curriculum for bioinformatics: the time isKolaskar, Vice Chancellor, KIIT, Bhubaneshwar (Founder ripe. Bioinformatics 1998;14:549–50.Director, Bioinformatics Centre and former Vice Chancellor, 13. Kulkarni-Kale U, Bhosle S, Manjari GS, et al. VirGen: aUniversity of Pune) for his mentorship and for exposing them comprehensive viral genome resource. Nucleic Acids Resto the exciting area of bioinformatics. The authors put on record 2004;32:D289–92.their sincere thanks to Dr T. Madhan Mohan, Senior Advisor, 14. Kulkarni-Kale U, Bhosle SG, Manjari GS, et al. Curation ofDBT for his efforts in strengthening the BTIS network in India. viral genomes: challenges, applications and the way forward.We gratefully acknowledge Dr S.R.R. Reddy for compilation BMC Bioinformatics 2006;7(Suppl 5):S12.and analysis of BINC statistics and for adding value to the manu- 15. Ghate AD, Bhagwat BU, Bhosle SG, et al. Characterizationscript. We thank Mr. Vivek Sawant, MD, MKCL, Pune of antibody-binding sites on proteins: development of afor review and value additions to the manuscript. We thank knowledgebase and its applications in improving epitopeDr P. S. Naik and Dr Shubhda Nagarkar for useful suggestions. prediction. Protein Peptide Lett 2007;14:531–5.
page 10 of 10 Kulkarni-Kale et al.16. Coulet A, Shah N, Hunter L, et al. Extraction of genotype- 19. Gaikwad J, Chavan V. Open access and biodiversity con- phenotype-drug relationships from text: from entity recog- servation: Changes and potentials for the developing world. nition to bioinformatics application. Pac Symp Biocomput Data SciJ 2006;5:1–17. 2010;485–7. 20. Holmes EC, Grenfell BT. Discovering the phylodynamics17. Friedman CP, Altman RB, Kohane IS, et al. American of RNA viruses. PLoS Comput Biol 2009;5:e1000505. College of Medical Informatics. Training the next genera- 21. Hey T, Tansley S, Tolle K, (eds). The Fourth Paradigm: Data tion of informaticians: the impact of ‘‘BISTI’’ and bioinfor- intensive scientific discovery. Washington, USA: Microsoft matics–a report from the American College of Medical Research, Redmond, 2009;1–241. Informatics. J Am Med Inform Assoc 2004;11:167–72. 22. Butler D. Human genome at ten: Science after the18. Thorn CF, Klein TE, Altman RB. Pharmacogenomics and sequence. Nature 2010;465:1000–1. bioinformatics: PharmGKB. Pharmacogenomics 2010;11: 501–5. Downloaded from http://bib.oxfordjournals.org at New Copenhagen University on August 20, 2010