Transcript annotation in FANTOM3: Mouse gene catalog based on physical cDNAs

T he international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched cDNAs. The previous dataset, FANTOM(2), comprised 60,770 full- length enriched cDNAs. Functional annotation revealed that this cDNA dataset contained only about half of the estimated number of mouse protein- coding genes, indicating that a number of cDNAs still remained to be collected and identified. To pursue the complete gene catalog that covers all predicted mouse genes, cloning and sequencing of full- length enriched cDNAs has been continued since FANTOM2. In FANTOM3, 42,031 newly isolated cDNAs were subjected to functional annotation, and the annotation of 4,347 FANTOM2 cDNAs was updated. To accomplish accurate functional annotation, we improved our automated annotation pipeline by introducing new coding sequence prediction programs and developed a Web- based annotation interface for simplifying the annotation procedures to reduce manual annotation errors. Automated coding sequence and function prediction was followed with manual curation and review by expert curators. A total of 102,801 full- length enriched mouse cDNAs were annotated. Out of 102,801 transcripts, 56,722 were functionally annotated as protein coding ( including partial or truncated transcripts), providing to our knowledge the greatest current coverage of the mouse proteome by full- length cDNAs. The total number of distinct non- protein- coding transcripts increased to 34,030. The FANTOM3 annotation system, consisting of automated computational prediction, manual curation, and. nal expert curation, facilitated the comprehensive characterization of the mouse transcriptome, and could be applied to the transcriptomes of other species.

Sharing Narratives Online: An international, self-organising curriculum in rural health

The aim of the Rural Medicine Rotation (RMR) at the University of Queensland (UQ) is to give all third year medical students exposure to and an understanding of, clinical practice in Australian rural or remote locations. A difficulty in achieving this is the relatively short period of student clinical placements, in only one or two rural or remote locations. A web-based Clinical Discussion Board (CDB) has been introduced to address this problem by allowing students at various rural sites to discuss their rural experiences and clinical issues with each other. The rationale is to encourage an understanding of the breadth and depth of rural medicine through peer-based learning. Students are required to submit a minimum of four contributions over the course of their six week rural placement. Analysis of student usage patterns shows that the majority of students exceeded the minimum submission criteria indicating motivation rather than compulsion to contribute to the CDB. There is clear evidence that contributing or responding to the CDB develops studentâ??s critical thinking skills by giving and receiving assistance from peers, challenging attitudes and beliefs and stimulating reflective thought. This is particularly evident in regard to issues involving ethics or clinical uncertainty, subject areas that are not in the medical undergraduate curriculum, yet are integral to real-world medical practice. The CDB has proved to be a successful way to understand the concerns and interests of third year medical students immersed in their RMR and also in demonstrating how technology can help address the challenge of supporting students across large geographical areas. We have recently broadened this approach by including students from the Rural Program at The Ohio State University College of Medicine. This important international exchange of ideas and approaches to learning is expected to broaden clinical training content and improve understanding of rural issues.

A new breed of doctor? Lessons learned and changes made to library services for the MBBS program at the University of Queensland

November 2000 saw the graduation of the first cohort from the new MBBS Program at The University of Queensland. The fully integrated problem-based curriculum has provided many challenges and opportunities for The University of Queensland Library such as servicing an extensive remote student population, information technology issues and customer demand. In October 2000 all four years of the MBBS Program completed a survey on related issues such as the library's collection, web-based resources, information skills and evidence-based medicine. This paper focuses on the results of the survey, and the future directions of the library to ensure that the new doctors graduating from this program gain the essential attributes of life-long learning, information management and evidence-based principles.

Fostering professional development through integrating work and formal learning

The Undergraduate Site Learning Program (USLP) is an innovative work-based learning program that addresses the call to develop a broader set ofattributes in engineering graduates. Unlike cooperative education programs, site learning can give students full academic credit for their placement without extending the duration of the degree through the use of an innovative learning alignment model. A cenrralpart ofthis program is a unique course entitled Professional Development in which students articulate and reflect upon the lessons they leom while on placement in industry. Students spend the bulk ofa semester on-site often in remote locations, which requires a flexible approach to course operation and fosters independent learning. Thus the USLP challenges both staff and students and produces outcomes that bofh the alumni and industry value.