Bioinformatics

Article By

Rajesh kumar.R

MSc.,Bioteh,M.Phil.,Biotech,PGDBI,PGDIPR

INTRODUCTION

The 'first' convergence of computer and communication technologies in the latter half of the last century resulted in networks in general and the Internet in particular. The result of the first convergence, i.e. network technologies, is now converging with biomedical and genetic technologies to give rise to the second convergence. Consequently, an unprecedented increase in the quantity of information is being produced from genetic laboratories all over the world. This exponential increase in the quantity of information seems to be a phenomenon similar to that of the 'information explosion' after World War II, referred by Bowles (1999, p. 156). The phenomenal quantity of information (or merely of data?) currently being produced as a result of the second convergence can therefore be called the 'second information explosion'. In the light of this second information explosion and the coming of age of the information society in many parts of the world, we can evidence the emergence in the last three decades of bioinformatics.

WHAT IS BIOINFORMATICS?

The question that comes to the mind every time the term 'bioinformatics' is uttered is, 'what indeed is bioinformatics?' It is more than two decades now that this term has been used but a consensus definition still eludes, even when a large quantity of literature spanning many disciplines is being produced in both printed and digital form (Jeevan, 2002). The rise of undergraduate and advanced degree and training programmes in bioinformatics all over the world has been phenomenal (Altschul, 2005). In this burgeoning field, it is becoming increasingly difficult to establish what are or will be the essentials [of bioinformatics]. The readers of this volume will have a role in defining bioinformatics' future. (Altschul, 2005) It is not that there have not been attempts to define the emerging subject. The origin of many subjects at the end of the last century and in the 21st century is cross-disciplinary in nature, and bioinformatics does not seem to be an exception to this phenomenon. The cross-disciplinary nature of bioinformatics is evident in the words of Critchlow et al. (2000): Depending on whom you ask, bioinformatics can refer to almost any collaborative effort between biologists or geneticists and computer scientists - from database development, to simulating the chemical reaction between proteins, to automatically identifying tumors in MRI images. Attwood and Parry-Smith (2001, pp. 2-3) trace the context of evolution of the term as follows: During the last decade, molecular biology has witnessed an information revolution as a result of both of the development of rapid DNA sequencing techniques and of the corresponding progress in computer-based technologies, which are allowing us to cope with this information deluge in increasingly efficient ways. The broad term that was coined in the mid-1980s to encompass computer applications in biological sciences is bioinformatics. The emergence of bioinformatics as a cross-disciplinary subject has been well recognized. Biologists and geneticists were the first ones who started on the path that we today call bioinformatics. People from many other subjects, such as computer scientists, mathematicians and statisticians joined the bandwagon. The initial intended meaning of the term bioinformatics was the application of computers and associated machines for handling, storing and manipulating biological data. As Attwood and Parry-Smith (2001, p. 3) further point out, the term bioinformatics has been commandeered by several different disciplines to mean rather different things . . .. In the context of genome initiatives, the term was originally applied to the computational manipulation and analysis of biological sequence data (DNA and/or protein). Going through various definitions of this term, it appears that "the term 'Bioinformatics' is not really well-defined" (Weizmann Institute of Science, 200?) and many definitions are simply descriptions of activities carried out under this name. Some of the following identify subject areas where the term can be used, while others specify activities. It is used synonymously and interchangeably with computational biology, genetics, genomics, and molecular biology. Altschul (2005) commented on the growth and development of bioinformatics in the Foreword to the collected papers of the National Conference on Bioinformatics Computing, held in March 2005 at Patiala, India. But it can safely be said, from the above definitions (strict, loose, functional, etc.) and descriptions, that bioinformatics is concerned primarily with all aspects of the lifecycle of genetic and related data and information after its generation, such as its retrieval, dissemination, interpretation, and interrelation with other information (largely biological), in "converting it into knowledge." (Liebman, 1995). A diverse pattern emerges out of the above definitions that show the variety of activities covered under this term. Therefore, it is like a umbrella term, with every activity dealing with genetic and associated information for various purposes being covered under the bioinformatics umbrella. People from many disciplines are now coming together under this umbrella as tools-suppliers. The need of the hour is to evolve a cross-disciplinary definition that incorporates the concerns of all disciplines that have been contributing to this emerging subject.

INDIAN BIOINFORMATICS

Bioinformatics has the potential to be one of the fastest growing part of the Indian economy, after considering the factors like bio-diversity, human resources, infrastructure facilities and government's initiatives. International Data Corporation (IDC) has been reported that the pharmaceutical firms and research institutes in India are looking forward for cost-effective and high-quality research, development, and manufacturing of drugs with more speed. Moreover, Studies of IDC points out that India could capture the 8 per cent of the global bioinformatics market by 2008-09. The Indian Bioinformatics market was US $ 15 million as estimated by IDC in 2001. Growing at a compound annual growth rate (CAGR) of 20 per cent, the market size in 2003- 04 was around US $ 22 million. Indian Bioinformatics is in its nascent stage, only 6-7 yeas old. According to the survey conducted by CII Out (2005) of all the present companies 15.4 per cent are 5 years old, 23.1 are 3 years old and 61.5 per cent are only 2 years old. These companies are well diversified: 22 per cent are working in bioinformatics software development and another 22 per cent are working for molecular sequence analysis and data mining. The next major area is functional genomics in which 19 per cent of the companies are involved and 11 per cent of the firms are such that they are working in all the areas mentioned. The CII survey results also show that only 20 per cent of the companies in the sample are working exclusively in Bioinformatics. For 80 per cent of the companies, Bioinformatics is just a part of the business. Pure cost benefits for the biotech companies will definitely drive the bioinformatics field in the country. The biotech industry in 2000 has spent an estimated 36 percent on R & D. Success for many will mean a drastic reduction in R&D costs. Thus biotech companies will be forced to outsource software rather than developing propriety software like in the past. Since the cost of programs for handling this data is extremely high in the west, Indian IT companies have a great business opportunity to offer complete database solutions to major pharmaceutical and genome-based biotech companies in the world. The IT industry can also diversify its business focusing more on genomics through different levels of participation areas such as hardware, database product and packages, implementation and customization of software, and functionality enhancement of database. Abraham Thomas, managing director, IBM India Ltd, says, "the alignment of a vast pool of scientific talent, a world-class IT industry, a vigorous generic pharmaceutical sector and government initiatives in establishment of public sector infrastructure and research labs are positioning India to emerge as a significant participant on the global bioinformatics map."(BioSpectrum 2005) With an objective to help and rise bioinformatics sector to the world map the Bioinformatics Society of India (Inbios) has been working since August 2001. The Inbios already has over 270 members in a short span of one and half years. It has become a common informal platform for the younger generation to learn and contribute to this sun rising field in India. Next to these opportunities, it is also necessary to identify few problems that India shells solve to find a real advantage in the bioinformatics. The identifiable areas are in computation biology and bioinformatics, where a substantial level of development skills are required to develop custom applications to knot together and integrate disparate databases (usually from several global locations), simulations, molecular images, docking programs etc. The industry people, meanwhile, say that the mushrooming of bioinformatic institutes is creating a problem of finding talented and trained individuals in this industry. While many of them has a superficial knowledge and a certificate, India lacks true professionals in this area. Most people, who opt for bioinformatics are from the life sciences areas that do not have exposure to the IT side of bioinformatics, which is very important. Another issue is that some companies face shortage of funds and infrastructure. The turn around time for an average biotech industry to breakeven would be around three to five years. Most of the venture capitals and other sources of funding would not be very supportive, especially if the company is not part of a larger group venture. It would help if the government would take an active role in building infrastructure and funding small and medium entrepreneurs.

THE BANGALORE AGGLOMERATION

At this step, we want to point out the attention towards the geographical agglomeration of the bioinformatics in India. The most developed area is in the South India and, in particular, Bangalore and Karnataka Region. We are interested to incorporate culture and ethnicity as independent variables in location decisions in order to explain the regional concentration. Literature on the history and anthropology of India has also been consulted. There are two sub-question belonging to the location argument, which are tested empirically through secondary data from existing interview-based. Firstly, some ethnic and cultural groups in India apparently are more prone to knowledge-intensive industries due to their higher appreciation of learning. There are diverse culturally rooted attitudes towards education and technological as well as economic change. Secondly, the 'regional' culture of the South seems to be also more open in the sense of accommodating entrants from elsewhere - thereby converging initially diverse populations to a 'monocultural' one (cf. Klemm et al., 2005). There is a general misconception of 'the Hindu culture' or attitude towards modernization and innovation. Economists arrived at the crude conclusion that in principle it impedes the modernization of the Indian economy (e.g. Akerlof, 1976; Lal, 1988) not acknowledging existing anthropological fieldwork. While this pessimistic view of traditional 'cultures' has been restated in more general fashion in the collection of essays edited by Harrison and Huntington (2000), there are also more nuanced discussions of the interplay between culture and the economic realm (e.g. Rao and Walton, eds., 2004). Recently, there is more than anecdotal evidence that new Indian enterprises are determined even by the formerly priestly Brahmin caste rather than Vaishyas, the traditional business caste (Das, 2001). It might result from the fact that Brahmins have been involved more generally with activities relating to knowledge (Sen, 1997). Earlier Brahmins had a much more negative attitude towards business, trade and commerce in general (Adams, 2001; Rutten, 2002). With regard to South India there are a few notable deviations. Primarily, there have always been high-caste non-Brahmins pertaining to the indigenous population who were not only engaged with the learning of their sacred scripts but 'who were adept in Sanskrit learning as well' (Stein, 1999: 52). Hence, the foundations for a knowledge-based society have existed in South India ever since and, moreover, have been much more diffused throughout the broader society. Secondly, and related to the first, the population of the South is said to be much more homogenous than in the North. For instance, political movements in favor of backward groups started much earlier in South India and led to a more equal pattern compared to the still traditionally dominated, hierarchically oriented North (Jaffrelot 2002). Altogether, the Southern part of India seems to exhibit a more distinct regional culture of learning, not only in the sense of the regional development literature (Gertler 1997) but also literally. Apparently, this attitude is a solid foundation for the absorptive capacity necessary in order to adapt to new technologies. Although institutions of higher education have been allocated evenly over the whole country, there is a more than proportionate share of colleges, especially for engineering, and enrolment in the South (Chalam, 2000) (see tab. 1).

Table 1: Number of engineering colleges and enrolment compared to population Region Engineering collegesI EnrolmentI PopulationII No. National share Sanctioned capacity National share National share Central 50 7,54% 9,470 6,05% - East 25 3,77% 4,812 3,07% 25,8% North 140 21,12% 25,449 16,26% 31,3% West 140 21,12% 34,165 21,83% 19,6% South 308 46,46% 82,597 52,78% 23,2% Total 663 100,00% 156,493 100,00% 100,00%
I Source: Arora & Athreye (2002) II Source: Dossani (2002)

The regional distribution seems to be influenced by historical and geographical factors, at least to a certain extent. There are explanations like university-industry linkages with the premier research institutes, the establishment of Science - Technology Parks (STPs) close to the IITs and the IISc, as well as historical circumstances that led to the initial localizations. The historical factors rest in the early localization of science and technology related research and teaching institutions in Bangalore as an ideal place in terms of climate and infrastructure to conduct scientific research in strategic areas like defense and electronics. What is more surprising, however, is the distribution of socio-cultural and ethnic background. There have never in Indian history been so many entrepreneurial and managerial Brahmins as are seen in the bioinformatics now, and especially there have been few entrepreneurs from South India (Fromhold-Eisebith 1999; Kapur & Ramamurti 2001). Generally speaking, Brahmins were rather associated with priestly tasks, government jobs, all sorts of administration and landholding (Adams 2001). On the other hand, Brahmins as members of the priestly caste were always connected to all sorts of scholarly activities being related to knowledge, learning and teaching, like mathematics, but the brahminical education includes other sciences like grammar, geometry and logic (Sen 1997). Hence, there are many disciplines that are very useful for intellectually challenging professions like sciences or research related pharmaceuticals, biotechnology or software. Moreover, the combination of the subjects emphasized by a brahminical syllabus seems to be especially apt for bioinformatics, which requires not only mathematics but also language. Being handed down from one generation to the next for decades or even centuries would place descendants in a privileged position regarding such professions and, thus, be an example for a regional culture. Eventually, this has been compounded by land ownership and political power. Deshpande (2000) calls a cumulative advantage that the upper castes today are in such a strong position that in order to retain their privilege they do not need the customary inheritance of status anymore. However, a dominant position in administration could have been used in order to assure a more than proportionate share of Brahmins in high schools and universities (Adams 2001). But even if Brahmins have monopolized learning there might be a positive impact on the Indian economy in the 'knowledge age' (Das 2001). In addition what is unexpected is the relative under-representation of Vaishyas, the traditional group of entrepreneurs, although recent studies do not show a significant change in this occupation pattern (Deshpande 2000; Adams 2001). They have always been the entrepreneurial castes of the Hindu population providing economic services like trading, money lending (Rutten 2002). One explanation resides in the attitude of the traditional merchants and trader class towards risk and quick profits. They often prefer the latter and avoid taking risks, thus foregoing higher profits in the longer term (Frederking 2002). In the same vein, what follows for the ethnic background might simply be an eventual consequence - a path dependent process that resulted in a lock-in in South India. However, as has been argued above, these Southern states exhibit not only a higher appreciation of learning but also a more hospitable climate towards change, both technological and social.

THE BIOINFORMATIC MANPOWER

Considering that India has a large pool of scientific talent available at reasonable cost, a strong IT skilled, English speaking population, huge bio-diversity and a large number of research and development institutes, it would have a big role to play in the sunrise of Bioinformatics. A true Bioinformatician is the one who can form biological questions and find answers to those using Bioinformatics as tools. His objective should be to get real time solutions. There is enough demand for Bioinformaticians but the demand is of quality people who are not available. Software for a particular experiment can be structured into algorithms with fed in combinational results, so that the life scientist is able to get a result, which may have taken him much longer otherwise. But in all this what is required is the ability for either of these parties to communicate each other. Therefore, there is need for people from the Biology, Chemistry and other pure science background to work in a team with computer professionals. What is important to note here is that both these fields have absolutely different work ethics. While a computer scientist will take in a mathematical and set language, a biologist will take time to understand a sequence; he will be involved in research that may not result into a discovery over night. This is the importance of Bioinformatics creeps in. As Bioinformatics involves software development and/or implementation for storage and analysis of a vast amount of biological data, the professionals in the field are required to have the following skills:

· In depth programming · In depth knowledge of biology · Relational database skills

Most of the bioinformatics companies prefer people from physics, molecular biology, mathematics, statistics or computer science background rather than biologists turned programmers. Otherwise, it creates isolated groups that have little interaction with molecular biologists and biochemists, which will ultimately fail to achieve promise of better understanding of biology. Next to these good perspectives that we talked till now, we need to discuss the main deficiencies that are found in the Bioinformatics manpower. Despite the large availability of workforces, India is facing a shortage of "skilled" manpower in this field. Part of it is contributed by lack of high-end research and concentration on only product/process based research. Human capital in India is available in abundance, and this can be a boon if adequate efforts are made to train, preserve and retain the available manpower. Industry strongly feels that the available manpower is quite sufficient in number but it seriously lacks in the terms of skills. The reason behind this is most of the institutes and colleges are misusing this new hype. While the awareness is low, a huge number of inappropriately designed courses have been started. Students who cannot enroll themselves in High Graduate Institutes (like Pune University, Institute of Bioinformatics and Applied Biotechnology, JNU etc.) join courses in sub-standard institutes, getting degrees and creating more and more non-employable students, hence creating the wide resource gap in the field. Therefore, the Government needs to ensure that the courses, which are carefully designed and include relevant training experience should only get license to operate.

THE KLEPPER VIEW AND INDIAN BIOINFORMATICS

The geographical concentration can emerge for several reasons and usually it is explained by agglomeration economies involving knowledge spillovers across co-located companies to demonstrate a persistent regional leadership. A different theory, with many practical examples, argued by Klepper, shows that geographical concentration can emerge as a natural consequence of the clustering of early leaders in certain narrow regions without any agglomeration economies. Klepper's findings also indicate an important role for related industries in producing the initial group of successful firms and for the persistence of the early leaders (for example the case of tire industry agglomerated around a small northeastern Ohio city, Akron, with no compelling advantages for tire production but just with a tradition in the production of rubber). Geographical concentration and persistence of leading firms are closely related. So it appears - even for India - comparative advantage (English speaking, low cost of labor, etc.) is simply a necessary but not sufficient condition for explaining a good condition in the international market. One way to think this issue is, in addition to the comparative advantage, to be successful it is necessary distinctive sources of competences to breed successful firms. This interplay between macro and micro, between comparative advantage at the country level and organizational capabilities at the firm level, is the right framework. In the Indian bioinformatics, this theory can explain the origin of a significant percentage of the global market with the diversification from the Indian IT leaders. In fact, as we see before, the bioinformatics competences are very close to IT skills. And with the high performance of software leaders (the most important are TCS, Kshema Technologies, V-Moksha and Wipro), they decided to invest in this new field and now they are one of the best companies in this area.
Next to this condition it is important to underscore also the presence of several spin-offs from these leaders even if only a few percentage has a persistence in the market. Next to the organizational capabilities of IT leaders and their diversification towards bioinformatics is the primary reason to this concentration of companies in the Bangalore Area and moreover in Karnataka, it is relevant also to look at the government policies, which help to exchange the science competences in a smooth way in an already dynamic context.

The Wipro case

Wipro Technologies was ranked 21st worldwide among software services companies, and 86th in terms of best performing technology companies by BusinessWeek in 2002 and 2001. The company's IT business began in 1980, and by 2002 had about 12,000 employees operating out of 27 offices worldwide. With $736 million in revenues in 2001-2002 and a CAGR of 45 percent over the last five years, Wipro was one of the major success stories of the Indian IT industry (http://www.wipro.com/). In April 2002, Wipro CEO Azim Premji created Wipro Health Care and Life Sciences, a wholly-owned subsidiary located in Bangalore. This business addressed the requirements of the "bio-IT market," which Wipro defined to include traditional IT services to hospitals, health insurance companies, and medical and analytical devices companies as well as to players in the drug discovery value chain. Wipro estimated this market to be about $25 billion, growing at over 20 percent annually. Wipro's application of IT to drug discovery (or "pure BI") was still a relatively small part of its business, and most of their efforts were in the traditional IT service areas of outsourcing operations, IT consulting and enterprise package implementation in health care sector companies. Wipro Healthcare and Life Sciences had about 250 employees. Over the course of 2002, the company's plans to attack the pure BI market underwent some changes. The original plan to go after large pharmaceutical companies to offer customized software had evolved into a strategy based on partnering with other firms to integrate domain and IT knowledge. The CEO of the health care and life sciences business had said, "Though we have experience in this area, gained from our association with GE Medical, we would like to focus more on the domain knowledge side, where partners would bring in the necessary strength." The company was interested in concentrating on IT support for clinical trials, data management and statistical analysis. The partners would help in providing the necessary support services to accelerate the drug discovery process and generate data on chemical compounds. In the drug discovery stage, for example, Wipro wanted to work as a technology partner for large consortia of life science equipment vendors who supplied the equipment that aids the drug discovery process. Wipro would help in synchronizing the data that these equipment churned out so that customers would not need to custom design them using their in-house IT resources. In the drug approval phase, Wipro intended to capitalize on the FDA's plans to allow electronic filing of Investigational New Drug (IND) reports by pharmaceutical companies. Wipro would use its knowledge of Web solutions, data security and imaging technology to assist customers in the electronic filing process.

CONCLUSIONS

With the convergence of genetics and computers, the increase in the quantity of information being produced from genetic laboratories constitutes a 'second information explosion'. As a result of this convergence, bioinformatics has emerged as a transdisciplinary subject with literature on it being produced in many established disciplines. We focused our attention on the position of Indian Bioinformatics, which is just in the first steps. We analyzed the condition of the Bangalore area from an anthropologic point of view to explain a positive correlation between the South Indian culture and the knowledge economy, and in particular with Bioinformatics. Moreover, we explained the rise of a cluster of bioinformatics companies in the same area also using the Klepper's theory about the use of specific capabilities of a developed industry (IT), also with the example of Wipro.