The life sciences Global Image Database (GID).
Although a vast amount of life sciences data is generated in the form of images, most scientists still store images on extremely diverse and often incompatible storage media, without any type of metadata structure, and thus with no standard facility with which to conduct searches or analyses. Here we present a solution to unlock the value of scientific images. The Global Image Database (GID) is a web-based (http://www.gwer.ch/qv/gid/gid.ht m ) structured central repository for scientific annotated images. The GID was designed to manage images from a wide spectrum of imaging domains ranging from microscopy to automated screening. The annotations in the GID define the source experiment of the images by describing who the authors of the experiment are, when the images were created, the biological origin of the experimental sample and how the sample was processed for visualization. A collection of experimental imaging protocols provides details of the sample preparation, and labeling, or visualization procedures. In addition, the entries in the GID reference these imaging protocols with the probe sequences or antibody names used in labeling experiments. The GID annotations are searchable by field or globally. The query results are first shown as image thumbnail previews, enabling quick browsing prior to original-sized annotated image retrieval. The development of the GID continues, aiming at facilitating the management and exchange of image data in the scientific community, and at creating new query tools for mining image data. (+info
Singapore focuses its life science strategy on humans.
The tiny island has invested heavily in life sciences as a linchpin of its future economy. But initial enthusiasm for a broad-based approach has switched to a focus on human healthcare, reports Kenneth Lee. (+info
Nutrition: a reservoir for integrative science.
In the last twenty years, powerful new molecular techniques were introduced that made it possible to advance knowledge in human biology using a reductionist approach. Now, the need for scientists to deal with complexity should drive a movement toward an integrationist approach to science. We propose that nutritional science is one of the best reservoirs for this approach. The American Society for Nutritional Sciences can play an important role by developing and delivering a cogent message that convinces the scientific establishment that nutrition fills this valuable niche. The society must develop a comprehensive strategy to develop our image as the reservoir for life sciences integration. Our efforts can start with our national meeting and publications, with the research initiatives for which we advocate, with our graduate training programs and with the public relations image we project for ourselves. Defining the image and future directions of nutrition as the discipline that can integrate scientific knowledge from the cell and molecule to the whole body and beyond to populations can be the most important task that our society undertakes. If we do not effectively meet this challenge, a golden opportunity will pass to others and nutritional scientists will be left to follow them. (+info
DNA Data Bank of Japan (DDBJ) for genome scale research in life science.
The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has made an effort to collect as much data as possible mainly from Japanese researchers. The increase rates of the data we collected, annotated and released to the public in the past year are 43% for the number of entries and 52% for the number of bases. The increase rates are accelerated even after the human genome was sequenced, because sequencing technology has been remarkably advanced and simplified, and research in life science has been shifted from the gene scale to the genome scale. In addition, we have developed the Genome Information Broker (GIB, http://gib.genes.nig.ac.jp) that now includes more than 50 complete microbial genome and Arabidopsis genome data. We have also developed a database of the human genome, the Human Genomics Studio (HGS, http://studio.nig.ac.jp). HGS provides one with a set of sequences being as continuous as possible in any one of the 24 chromosomes. Both GIB and HGS have been updated incorporating newly available data and retrieval tools. (+info
Fruits of human genome project and private venture, and their impact on life science.
A small knowledge base was created by organizing the Human Genome Project (HGP) and its related issues in "Science" magazines between 1996 and 2000. This base revealed the stunning achievement of HGP and a private venture and its impact on today's biology and life science. In the mid-1990, they encouraged the development of advanced high throughput automated DNA sequencers and the technologies that can analyse all genes at once in a systematic fashion. Using these technologies, they completed the genome sequence of human and various other organisms. These fruits opened the door to comparative genomics, functional genomics, the interdisprinary field between computer and biology, and proteomics. They have caused a shift in biological investigation from studying single genes or proteins to studying all genes or proteins at once, and causing revolutional changes in traditional biology, drug discovery and therapy. They have expanded the range of potential drug targets and have facilitated a shift in drug discovery programs toward rational target-based strategies. They have spawned pharmacogenomics that could give rise to a new generation of highly effective drugs that treat causes, not just symptoms. They should also cause a migration from the traditional medications that are safe and effective for every members of the population to personalized medicine and personalized therapy. (+info
Science at a crossroads.
Science is entering an alliance with the economy that will speed the effect of innovation through society. Despite the slowdown of the 'new economy', a cascade paradigm of innovation appears key to increasing the rate of economic growth. Yet for science to continue to thrive and make this contribution to innovation, it must traverse at least three key crossroads. First, while life sciences have built a strong advocacy model to secure growing federal research funding, the physical sciences (including mathematics and engineering) have not and must now do so to thrive. Second, the drop in the numbers of physical scientists and engineers must be reversed if we are to have the talent to maintain a strong trend of scientific advance. Third, although science advances are increasingly interdisciplinary and occurring in the space between the historic science stovepipes, the organization of federal science support is largely unchanged since the beginning of the cold war. While a decentralized model has value, we must also consider new approaches that encourage deeper cooperation across science sectors and agencies. (+info
The Bioperl toolkit: Perl modules for the life sciences.
The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort. (+info
Inquiry-based undergraduate teaching in the life sciences at large research universities: a perspective on the Boyer Commission Report.
The 1998 Boyer Commission Report advocated improvement of undergraduate education at large research universities through large-scale participation of undergraduates in the universities' research mission. At a recent conference sponsored by the Reinvention Center, which is dedicated to furthering the goals of the Boyer Commission, participants discussed progress toward these goals and recommendations for future action. A breakout group representing the life sciences concluded that independent research experience for every undergraduate may not be feasible or desirable but that transformation of lecture courses to more inquiry-based and interactive formats can effectively further the Commission's goals. (+info