Bio Suite as teaching platform in a virtual environment

Usha Manne, Sowjanya Gvl, Meenakshi Pradhan, Harini Srinivasan, Navneet Bung, Rajgopal Srinivasan and Gopalakrishnan Bulusu

TCS Innovation Labs (Life Sciences Division) TATA Consultancy Services Limited,

1 Software Units Layout, Madhapur, Hyderabad 500 081, India. e-mail: gopal@atc.tcs.com

Abstract—Bio Suite is a comprehensive Bioinformatics software package developed under a unique academia-industry collaboration. The product is hosted on Amazon cloud for easy access to users from anywhere. Bio Suite is an efficient and easy to use state of the art Bioinformatics analysis package that is well suited to be a good teaching tool. Exploiting this feature of Bio Suite, a complete web course has been designed, which describes in detail both basic and advanced concepts in Bioinformatics. This web course is proposed to be hosted on “Knome” a TCS Knowledge Ecosystem Solution, based on social networking concepts, for learning and sharing. The availability of the web course on a user friendly platform, supported by Bio Suite deployed on cloud should make the learning experience easy and enjoyable for students.

Keywords-Bioinformatics; teaching; course; cloud; Knome; Bio Suite.

I. INTRODUCTION Bio Suite [1, 2] is a comprehensive suite of tools for

Bioinformatics analyses. The software has been developed by Life Sciences Division of the TCS Innovation Labs, Hyderabad at Tata Consultancy Services Ltd., in collaboration with Council of Scientific and Industrial Research (CSIR), India [3] and several leading Indian academic institutions, under the New Millennium Indian Technology Leadership Initiative program.

In the present era, students display great enthusiasm in learning, sharing and collaborating through networks. Internet, social networking and rich web applications are a part and parcel of our lives. The desire to contribute to the learning community led us to the idea of designing a teaching/learning web course, based on Bio Suite, accessible through a versatile social networking platform. At TCS, we have a Knowledge Ecosystem Solution called Knome [4], developed by TCS Innovation Labs, Chennai, which we incorporate in this project.

II. PROBLEM STATEMENT Most commercial Bioinformatics and Computational

biology softwares are available only for local installation on a desktop or a powerful server. Moreover, the cost of licensing such softwares remain beyond the reach of most students. While there are excellent open source alternatives available, these still require download, installation and updates for effective use. Additionally, these are not organized as a course and therefore geared only for individualized learning. For beginners in the area of life sciences research, such bottlenecks restrict them in exploring the field of Bioinformatics. While books are definitely the prime source for concept building, utilizing

and applying the knowledge gained can only be possible through hands-on experience. Social networking, though primarily used for recreational purpose, can also serve as a good medium for interactive learning.

III. CONTRIBUTION In 2004, Bio Suite was launched as a desktop software

package. To facilitate the accessibility of Bio Suite for users worldwide, cloud technology has been employed. The application is currently deployed on Amazon Web Services (AWS) that can be accessed by anyone with an internet connection and an AWS account. The Bio Suite application on AWS is available on fedora flavor of Linux OS as a 32-bit processor instance. This service can be accessed from Windows, Mac or Linux platform. This also provides an opportunity for end-users to get exposed to cloud technology.

Utilizing the above technology, a web course has been designed that covers all aspects of Bioinformatics. This web course provides hands-on experience in functional areas of Bioinformatics. The topics covered range from genome analysis to protein modeling to drug design. The concepts and algorithms used at each level are explained with an example. The “Knome” platform allows students to peruse the web course interactively in a collaborative environment.

IV. DETAILS The purpose of this web course is to educate and

motivate beginners in the area of life sciences. Both Bio Suite, as a stand-alone package, and the web course were piloted in SASTRA University, Thanjavur and IIIT-H, Hyderabad and the feedback from students and instructors helped in improving the course content. The web course covers all major functionalities in Bioinformatics.

Mycobacterium tuberculosis Thymidylate kinase [5] is used as example to illustrate the concepts throughout the web course. The course includes a detailed study at sequence and structure levels leading up to modules for drug design (Figure 1).

Figure 1. Schematic representation of major functional areas of Bioinformatics covered in web course.

2012 IEEE Fourth International Conference on Technology for Education

978-0-7695-4759-6/12 $26.00 © 2012 IEEE

DOI 10.1109/T4E.2012.62

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A step by step explanation of carrying out the workflow (Figure 1) is provided in the web course. The availability of the web course on Knome (a collaborative platform) would encourage students to give productive remarks, exchange queries, and aims to provide a better environment for learning both by interacting within a community and in an open discussion forum (Figure 2).

V. RELATED WORK Many online resources are available for learning, of

which Scitable [6], a collaborative learning space for Science, provides tutorials that explain the biological concepts and has a good networking platform that helps users to communicate and collaborate among themselves. However, this platform does not have any Bioinformatics courseware. While resources like NCBI [7] tutorials provide a good hands-on experience in Bioinformatics, they lack a social learning and sharing platform. This inspired us to prepare a web course that could provide a good practical knowledge of Bioinformatics within a social networking environment.

VI. CONCLUSION Bio Suite, a comprehensive software package useful

for teaching purposes and academic research in the field of Bioinformatics, deployed on cloud has an advantage of easy access and can be launched from anywhere. A web course is developed to enhance learning of Bioinformatics

concepts, using this technology as a medium, in an interactive environment.

VII. FUTURE WORK We propose to streamline the project and pilot it in

few academic institutions. Later, we wish to proliferate it to all the academic institutions offering a Bioinformatics course.

ACKNOWLEDGMENT The authors thank Mr. K. Ananthkrishnan, CTO, TCS

for helpful suggestions, support and encouragement.

REFERENCES

[1] The NMITLI-BioSuite team, BioSuite: A comprehensive bioinformatics software package (A unique industry-academia collaboration). Curr. Sci., 92, 2007, 29-38. [2] http://tcsinnovations.com/hyderabad-solutions/526 [3] http://rdpp.csir.res.in/csir_acsir/Home.aspx [4] http://turing.web2labs.com/knome/whatsknome [5] B. Gopalakrishnan, V. Aparna, J. Jeevan, M. Ravi, and G. R. Desiraju, "A Virtual Screening Approach for Thymidine Monophosphate Kinase Inhibitors as Antitubercular Agents Based on Docking and Pharmacophore Models". J. Chem. Inf. Model, 45, 2005, 1101-1108,. [6] http://www.nature.com/scitable [7] http://www.ncbi.nlm.nih.gov/education/tutorials/

Figure 2. Outline of the proposed virtual Bioinformatics learning environment, using the web course on Knome linked to Bio Suite on cloud

technology.

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