News

Mon, 2012-07-30

The second event of the CodeForScience application development competition series concluded yesterday with CFS Talk & Awards, a thought leadership program featuring speakers across science, technology and research publishing sectors.

 

In addition to the application concept winners announced on June 5th, a total of six awards were given out to the teams that won the application development round. The winning applications were selected based on the evaluation criteria by the judging panel comprised of professors and information management experts from National Innovation Council, Indian Institute of Science (IISc), Indian Institute of Technology, Bombay (IITB), Johns Hopkins University (JHU), Institute of Genomics and Integrative Biology (IGIB), Madurai Kamaraj University, Institute of Microbial Technology, Strand Life Sciences and NVIDIA. For those who could not be with us at IISc Bangalore this past weekend, here goes the winning applications and demo videos:

 

 

  • Grand Prize: IntelliScholar (for ScienceDirect), developed by Pinaki Dey, Sudipta Sadhu and Rajiv Ram from Indian Institute of Technology, Bombay, shows the names of the authors with their latest and most-cited articles in tabular format. It also shows all references of the current article in an assorted order based on publication date. The main potential of IntelliSense unravels on pages related to life science, where user can search or select any Gene or Protein terms to open a hover window which will present a whole set of information as retrieved from databases like NCBI in a graphical manner.

 

  • Second Prize: ReachPathways (for ScienceDirect), developed by Babylakshmi M., Harsha Gowda and Joji Kurian Thomas from Institute of Bioinformatics, searches the ScienceDirect full text articles and retrieves the proteins in the article. By clicking on a protein, one can view the involvement of the selected protein in various pathways fetched from the popular pathway resources. The pathway resources include, 'NetPath', 'Reactome', 'WikiPathways', 'STKE' and 'NCI-PID'.

 

  • Third Prize: DISQUS Science (for ScienceDirect, Scopus and Hub), developed by Rishi Das Roy from Institute of Genomics and Integrative Biology, allows users to comment on an article, view those comments and reply back. Users can also share the articles, comments and rate the articles and comments. Subscription to a discussion-thread is also an option.

 

  • Excellence Award: BAITOC (for Hub), developed by B. Jayaram, Abhilash Jayaraj, Shashank Shekhar, and Goutam Mukherjee from Indian Institute of Technology, Delhi, stands for Bio-Activity Information To Organic Chemists. This application helps to assess the bio-activity of any organic compound by scanning a user specified organic molecule against a list of pathogen proteins to provide a list of top five pathogen protein information which are predicted to show the best bio-activity.

 

  • Excellence Award: LitMuS (for ScienceDirect), developed by Srinivas Srikanth from Institute of Bioinformatics, allows a user to study a gene of interest in the article by quickly browsing through the reported mutations, the primary tissues in which the study was done, and a link to NCBI PubMed. This application provides a bird's eye view of the mutational data pertaining to the gene of interest available in the COSMIC database.

 

  • Excellence Award: NetSlim (for ScienceDirect), developed by Joji Kurian Thomas from Institute of Bioinformatics, fetches protein names mentioned in the search results, abstracts, and full-text articles and links them to signaling pathways where the proteins appear based on the NetSlim database.

 

The winning applications will be available in the Applications Marketplace in the coming weeks.

 

 

 

Photograph by: FreeDigitalPhotos.net

Sat, 2012-07-07

CodeForScience, a global series of application development competitions for scientists, rising and experienced researchers and developers of diverse backgrounds, cordially invite you to CFS Talk & Awards India on Sunday, 29 July from 12 to 4:15pm at J. N. Tata Auditorium, Indian Institute of Science, Bangalore.

CFS Talk & Awards is an open forum for discussing tools and approaches that are influencing the re-design of researchers’ search and discovery experience. Attendees will have the opportunity to meet and discuss the changing research environment with leading researchers from academia, industry and government organizations. It's an unique event dedicated to advancing solutions for science, and all the more interesting as we will discuss the topics in context of India's talent. So come and join us. Listen in, speak up and raise questions about how you and your colleagues can benefit from these solutions or better yet, take a part in building them for the future.

This event is open to everyone. To reserve your seat, please register for your free tickets by July 29.

In addition to the thought leadership talks, CodeForScience participants will demonstrate their applications followed by announcement of the winners. 

PROGRAM

11:45 - 4:00 Registration & Networking
12:15 - 12:25 Welcome & Introductions
Debnath Pal, Ph.D., Associate Professor, Indian Institute of Science
12:25 - 1:50

Talks

  • The 21st Century Research Landscape: Emerging Trends in Scientific Publishing

Y. S. Chi, Chairman, Elsevier

  • Reinventing India through Science, Technology, Innovation, and Entrepreneurship

​Aravind Chinchure, Ph.D., Reliance Innovation Leadership Center

  • Best Practices for Creating Scientific Information Base for R&D Enterprises of Today & Future

​Ananda Byrappa, Global Leader, Knowledge Center, GE

  • Collaborative Innovation, Open Platforms & Workflow Applications

Vishal Gupta, Director, Developer Network, Elsevier

Debnath Pal, Ph.D., Associate Professor, Indian Institute of Science

  • Advancement of Computational Modeling in Sciences with Graphics Processing Units

Punit Kishore, HW Design Manager, NVIDIA

1:50 - 2:20 Refreshment Break
2:25 - 3:20

Panel Discussion

  • Science Your Way – Role of Customized Workflow Solutions 

​Moderator: Akhilesh Pandey, M.D., Ph.D., Professor, Johns Hopkins School of Medicine and Founder and Director, Institute of Bioinformatics

Panelists:

Debnath Pal, Ph.D., Associate Professor, Indian Institute of Science

Ramesh Hariharan, Ph.D., Co-Founder and Chief Technology Officer, Strand Life Sciences

Sanjeeva Srivastava, Ph.D., Assistant Professor, Indian Institute of Technology - Bombay

Gajendra P. S. Raghava, Ph.D., Scientist and Head of Bioinformatics Center, Institute of Microbial Technology

Soumitra Kumar Nandy, Ph.D., Professor, Indian Institute of Science

Debasis Dash, Ph.D., Scientist, Institute of Genomics and Integrative Biology

3:20 - 4:00 Application Demos
4:00 - 4:15 Award Presentation

 

SPEAKER BIOGRAPHY
in order of appearance in the program

Debnath Pal, Ph.D. Associate Professor, Indian Institute of Science
Debnath Pal currently serves as an Associate Professor at the Supercomputer Education Research Centre, Indian Institute of Science, Bangalore. He graduated with a M.Sc and Ph.D degree in Chemistry from Indian Institute of Technology, Kharagpur and Jadavpur University, Kolkata, respectively. Formally trained as a chemist, his deep desire to understand the relationship between chemical activity and molecular structure initiated him into the world of computing. His current research is interdisciplinary in nature, which combines the emerging areas of Omics and Computational Biology. He is recognized for his contributions in understanding molecular properties of proteins. He is a fellow of the Alexander von Humboldt Foundation, Germany and has won several honors, including the NASI-SCOPUS award (2010) co-sponsored by Elsevier. Dr. Pal devotes a significant amount of his time in promoting science and education in India, and his involvement in Code-for-Science, India is in the same spirit.

 

Y. S. Chi, Chairman, Elsevier
YoungSuk “YS” Chi is a leader in the media-tech industry.  As Chairman of the Elsevier Management Committee, he leads the development of information solutions that are transforming the STM industry.  He also oversees Corporate Affairs as well as Asia Strategy for Elsevier’s parent company, Reed Elsevier.  In addition, Chi serves as President of the International Publishers Association. Chi joined Elsevier in 2005 after serving as Chairman of Random House Asia and President of Random House.  Prior to Random House, he held several President and CEO positions at Ingram Distribution Holding, the parent company of Ingram Book Group, and co-founded Lightning Source, the book industry’s first ever print-on-demand and e-book distribution company.  Chi has served on numerous boards including that of Princeton University, and currently serves on the Executive Committees of the Association of American Publishers and the International Association of Scientific, Technical & Medical Publishers.

 

Aravind Chinchure, Ph.D., Asst. Vice President - Innovations, Reliance Innovation Leadership Center                                                                                                   Aravind Chinchure has a Ph.D. in Physics with 18 years experience in R & D, intellectual property, innovation, investment and business strategy. He has worked on diverse technology areas in the field of materials, chemistry, physics, electronics, renewable energy and information technology. Aravind is a member of the Sectoral Innovation Council of Ministry of Trade and Commerce, Government of India. He is a member of advisory council of the Institute of International Trade (IITrade), Kolkata. He is also Executive Member of the Tata Institute of Fundamental Research (TIFR) Alumni Association and Fellow of Society for Technology Management (STEM). Prior to joining Reliance industries, he has worked as a scientist at the General Electric (GE) Global Research Center, Bangalore, Leiden University, Netherlands, and TIFR, Mumbai.

 

Ananda Byrappa, Global Leader, Knowledge Center, GE                                                  Ananda Byrappa has a Master's degree in Information Science from Bangalore University. He did his Knowledge Management course at Indian Institute of Science, Bangalore. Ananda has spent over 15 years in top multinational corporates like Deutsche Bank Group and Zee Media Group. He is currently with GE, heading their Knowledge Center, which serves GE's 28 global sites in Asia, Europe and USA. He is a six sigma certified information professional. Ananda has served on the Scopus internaltional advisory board. He is a winner of Vikram Sarabhai Operation Excellence Award at GE India and is a certified Six Sigma Black-belt.

 

Vishal Gupta, Director, Developer Network, Elsevier
Vishal Gupta is the Director of Developer Network at Elsevier where he leads the effort to bring a paradigm shift in partnering with researcher and developer communities on Elsevier’s applications platform to jointly develop tools that are embedded deeply in user’s workflow, geared towards driving research outcomes and expand the information search and discovery experience for over 15 million users worldwide.  In his four years at Elsevier, Vishal has worked in different roles in product management, business development and in building strategic partnerships. Vishal holds an MBA from The Wharton School at the University of Pennsylvania and a BS from Delhi University.

 

Punit Kishore, HW Design Manager, NVIDIA                                                                     Punit Kishore has a B.Tech degree from IIT Kanpur in the field of Electrical engineering. Punit started his career at Texas instruments as a wireless hardware design engineer. After working for 1.5 years at Texas Instruments, he moved to join NVIDIA and started working on GPU and MCP designs. He has total experience of 8 years in the field of high speed VLSI design. Punit currently manages the high speed IO DFT group at NVIDIA. He has keen interest in high performance computing and have evangelized CUDA programming  in the Indian universities like IIT, CDAC, IISc.

 

Akhilesh Pandey, M.D., Ph.D. Professor, Johns Hopkins School of Medicine, Founder & Director, Institute of Bioinformatics
Akhilesh Pandey is currently a Professor at the Institute of Genetic Medicine and the Departments of Biological Chemistry, Oncology and Pathology at the Johns Hopkins School of Medicine. He obtained his M.D. from Armed Forces Medical College, Pune and completed his residency in Pathology at the Brigham and Women's Hospital, Harvard Medical School. He obtained his Ph.D. in the laboratory of Vishva Dixit at the University of Michigan, Ann Arbor in 1995 and carried out his Postdoctoral work in the laboratory of Harvey Lodish at the Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology from 1996-1999. He was a Visiting Scientist with Matthias Mann at the University of Southern Denmark from 1999-2002 before joining Johns Hopkins in 2002. He is a past Editorial Board member of Genome Research and currently serves as an Editorial Board member of Molecular and Cellular Proteomics, Journal of Proteome Research, Proteomics, Clinical Proteomics and DNA Research and as an Associate Editor of BMC Bioinformatics. He is also the Founder and Director of the Institute of Bioinformatics, a non-profit research institute in Bangalore, India.

Panelists

Debnath Pal, Ph.D., Associate Professor, Indian Institute of Science

Ramesh Hariharan, Ph.D., Co-Founder and Chief Technology Officer, Strand Life Sciences

Sanjeeva Srivastava, Ph.D., Assistant Professor, Indian Institute of Technology - Bombay

Gajendra P. S. Raghava, Ph.D., Scientist and Head of Bioinformatics Center, Institute of Microbial Technology

Soumitra Kumar Nandy, Ph.D., Professor, Indian Institute of Science

Debasis Dash, Ph.D., Scientist, Institute of Genomics and Integrative Biology

Wed, 2012-06-27

We organized several developer events in 2011 and early 2012, including the global challenge ‘Apps for Science’ and the national challenge ‘CodeforScience Turkey’. Below are some of the winning applications from these competitions. Your application could be a winner at CodeforScience India; so bring out your creative side to develop innovative applications in the Application Development Round and win many amazing prizes. All eligible entries from the Concept Formulation Round are now available for you. You are free to use any of these concepts to build your application.

 

AltmetricGrand Prize Winner at Apps for Science

Altmetric measures the attention that scientific articles receive on social media sites, in online reference managers and from mainstream news sources. This app adds data from Altmetric to the ScienceDirect & Sciverse Hub article and search result pages.

 

 

ChemDetectHonorable Mention at Apps for Science

Living directly next to articles on the full-text view, on your command ChemDetect will quickly scan an article for chemical names and draw full structures. Whether you are looking for visual insight or scrambling to piece together a presentation for your lab, ChemDetectwill stand by your side, tirelessly reading articles and rendering structures late into the night.

 

 

RefWizardFirst Prize Winner at CodeforScience Turkey

RefWizard is a visual reference explorer tool. It presents the references of a selected article on an interactive, dynamic graph. In this graph, each reference is represented by a node. Users can interact with RefWizard in several ways.

 

 

ApexSecond Prize Winner at CodeforScience Turkey

APEX is developed to give researchers a quick insight about authors works that they follow or research about. It helps researchers to track authors publication development, progress and process.

 

 

What is a SciVerse Application?

A SciVerse Application is basically a ‘gadget’ on the SciVerse platform. The Application Framework uses Apache Shindig (http://shindig.apache.org/)  which is based on OpenSocial specification. The Google gadgets API is also a part of this specification. SciVerse applications are defined in XML and they are wrappers around HTML and JavaScript.

Do you know how to build an application on the SciVerse platform? Watch the video to learn ‘How to Build a SciVerse Application’ 

 

 

If you would like to know more about the different datasets, tools, and APIs that you could use, please visit the Resources to get answers for all your questions. If there are any additional questions, please visit FAQ or Contact Us.

 

Cheers,

Team CodeforScience India

 

 

Photograph By: FreeDigitalPhotos.net

Tue, 2012-06-12

We would like to thank our sponsors – NVIDIA, Thermo Scientific, and Microsoft Research for their generous support for CodeForScience India which has been instrumental in the success of the competition so far.

 

NVIDIA – Platinum Sponsor

NVIDIA awakened the world to computer graphics when it invented the GPU in 1999. From its roots in visual computing, the company expanded into parallel computing and mobile computing. Today, its processors power a broad range of products from smartphones to supercomputers. NVIDIA's mobile processors are used in phones, tablets and auto infotainment systems. PC gamers rely on GPUs to enjoy spectacularly immersive worlds. Professionals use them to create visual effects in movies and design everything from golf clubs to jumbo jets. And researchers utilize GPUs to advance the frontiers of science with high-performance computers. The company holds more than 2,300 patents worldwide, including ones covering ideas essential to modern computing.

 

 

NVIDIA’s expertise in programmable GPUs led to breakthroughs in parallel processing. Scientists and researchers around the world are using Tesla graphics cards to tackle the most complex challenges, from climate modeling to quantum physics to finding a cure for cancer. NVIDIA CUDA architecture enables GPUs to work not just with the pixels of an image, but with numerical data. NVIDIA Tesla processors harness CUDA to make supercomputing more efficient and more accessible. Three of the top five supercomputers are powered by Tesla GPUs. And on the November 2011 list of Top500 supercomputers, the number of NVIDIA GPU-powered systems more than tripled in just a year, to 35. Learn more about GPU-accelerated applications available for astronomy, biology, chemistry, physics, data mining, manufacturing, finance, and more on the software solutions page.

Don’t forget – NVIDIA has special prizes for participants of Application Development Round.

 

Microsoft Research – Silver Sponsor

Microsoft Research is dedicated to conducting both basic and applied research in computer science and software engineering. Researchers focus on more than 55 areas of computing and collaborate with leading academic, government and industry researchers to advance the state of the art. Microsoft Research has expanded over the years to thirteen labs worldwide and a number of collaborative projects that bring together the best minds in computer science to advance a research agenda based on their unique talents and interests.

Don’t forget – Microsoft Research has special prizes for participants of Application Development Round.

 

Thermo Scientific – Silver Sponsor

Thermo Fisher Scientific Inc. is the world leader in serving science. Our mission is to enable our customers to make the world healthier, cleaner and safer. With revenues of $12 billion, we have approximately 39,000 employees and serve customers within pharmaceutical and biotech companies, hospitals and clinical diagnostic labs, universities, research institutions and government agencies, as well as in environmental and process control industries. We create value for our key stakeholders through three premier brands, Thermo Scientific, Fisher Scientific and Unity™ Lab Services, which offer a unique combination of innovative technologies, convenient purchasing options and a single solution for laboratory operations management. Our products and services help our customers solve complex analytical challenges, improve patient diagnostics and increase laboratory productivity.

 

ARE YOU READY TO BUILD YOUR APPS?

The Application Development Round is already rolling! This is your opportunity to showcase your talent and compete for exciting prizes by building creative and innovative applications. Whether you participated in the first round or not, we invite you to participate in the Application Development Round. You are free to use the concept you have submitted or work on a completely new idea. Winners of this round will not only receive amazing prizes, but their apps will be published on the Applications Gallery and made available to more than 15 million users globally. Developers can also receive direct user feedback and find future collaborators through the growing marketplace of new apps.

Do you know how to build an application on the SciVerse platform? Watch the video to learn ‘How to Build a SciVerse Application’ 

 

 

Please visit the Application Gallery to see the existing apps. If you would like to know more about the different datasets, tools, and APIs that you could use, please visit the Resources to get answers for all your questions. If there are any additional questions, please visit FAQ or Contact Us.

 

Cheers,

Team CodeforScience India

 

 

Photograph By: FreeDigitalPhotos.net