building biodiversity information education: next generation bioinformaticians p. bryan heidorn...
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Building Biodiversity Information Education: Next Generation Bioinformaticians
P. Bryan HeidornCarole PalmerDan Wright
Graduate School of Library and Information Science University of Illinois at Urbana-Champaign
Information Power Tool Training
• Who needs bioinformaticians?
• What is a bioinformatician?
• Who are the bioinformaticians?
• What do bioinformaticians need to know?
• Proposed training programs
Reports on cyberinfrastructure and e-science initiatives recognize the shortage in qualified professionals to manage the increasing stores of scientific data (National Science Board, 2005)
Who needs bioinformaticians?
What is a bioinformatician?
preparing information specialists to work in such “information-rich environments and to participate as peers in problem solving” requires cross training in library and information science and discipline knowledge of scientific domains. Florance et al. (2002)
Who are the bioinformaticians?
• Biologists at all degree levels self trained in information technology
• Information technologists at all degree levels self trained in biology (I.e. clueless for X months)
• Professional Bioinformaticians
Audiences for TDWG Training
• Practicing Biology Researchers• Practicing Computer/Information
Scientists• Bachelors/Masters/PhD Students
– Biology– CS– Biological Informatics
Settings
• Online Documentation– Standard itself– Primer– PowerPoint (added audio stream)
• Just in time • Workshops (e.g. DigIR training)• [A]Synchronous Distance Education
Granularity
• University training (Semester Granularity)– Masters in Biological Informatics (National
Science Foundation under Grant No. IIS-0534567 to Carole L. Palmer and P. Bryan Heidorn.)
– MSLIS Data Curation Concentration (Institute of Museum and Library Services RE-05-06-0036-06 )
– Individual Courses
What do bioinformaticians need to know
Abstract Skill Sets1) Evaluation and implementation of
information systems: user based assessment and continual quality improvement for the development of tools that work and are used.
2) Information acquisition, management, and dissemination: development of digital libraries, data archives, institutional repositories, and related tools.
3) Information organization and integration: ontology development, structuring information for optimal use and sharing, and standards development.
Six step plan
1) Spur interest in BDI education and outreach among TDWG members or potential members.
2) Develop and ever changing list of the knowledge and skills required in biodiversity informatics.
3) Define educational units which might include key documents, a bibliography, and optional venues to face-to-face and Internet classes.
Six step plan
4) Maintain pointers to relevant educational units where they exist outside of TDWG.
5) Make educational materials where they do not exist, so that it easy for prospective learners can most easily acquire the knowledge.
6) Identify the dependencies among required skills and knowledge so that learners can plot a meaningful path through educational units.
Technology dependencies
• What must you know to use a standard?• Darwin Core
– requires a transport layer (DigIR then TAPIR)
– XML editors/validators (not all equal XMLSpy, Oxygen, …)
• DigIR requires PHP, SQL• General Computational Compatency• TDWG pointers to learning about these
technologies
What do new students in botany, entomology, X-ology need to learn about computation before getting to your lab or museum?
What (if anything) falls beyond TDWG’s purview?
Biological Informatician’s Skill Sete.g. UIUC, MS in Bioinformatics
Core Requirements
Computer Science
Biology
Bioinformatics
CS 411: Database Systems CS 473: Algorithms
18 to choose from
(= computational biomolecular informatics)Applied BioinformaticsBioinformaticsLaboratory Techniques in BioinformaticsAlgorithms in bioinformatics**Principles of SystematicsComputing in Molecular BiologyGenomics, Proteomics, and Bioinformation
Concentration / Disciplinary
• Natural Science Ontologies• Science Communication• Biodiversity and Ecology Informatics
Representing and Organizing Information
Interfaces to Information Systems
Building Digital Libraries Indexing and Abstracting
Health Sciences, Information Services and Resources
Architecture of Networked Information Systems
Information Sources and Services in the Sciences
Implementation of Information Retrieval Systems
Use and Users of Information
Electronic Publishing
Document Modeling
Current CoursesNew this SemesterProposed
Scientific data and procedure standards Sociotechnical perspectives on scientific practice
Scientific classifi cation and vocabulary State-of-the-art informatics resources and tools Ontology development Scientific literatures and bibliometrics Data curation and long-term data management Open access repositories Discovery informatics and data mining Project management Interdisciplinary scientific collaboration
Biodiversity Informatics
• Data Quality and Data Curation• Natural History Museum Informatics• Social Factors in Data Sharing• Interactive Keys• Field Monitoring• Geographic Information Systems• Information Federation in Biology• Computational Ecology• Biodiversity Ontologies• Molecular Bioinformatics
Educational Objects
• Education materials are type 3 documents.
• Need templates.• Parts of educational objects
– Standard– Dependencies– Primer– Demonstrations– Exercises– …