Building Biodiversity Information Education: Next Generation Bioinformaticians

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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
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Information Power Tool Training

• Who needs bioinformaticians?
• What is a bioinformatician?
• Who are the bioinformaticians?
• What do bioinformaticians need to know?
• Proposed training programs

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Who needs bioinformaticians?

• 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)

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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)

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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

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Audiences for TDWG Training

• Practicing Biology Researchers
• Practicing Computer/Information Scientists
• Bachelors/Masters/PhD Students
• Biology
• CS
• Biological Informatics

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Settings

• Online Documentation
• Standard itself
• Primer
• PowerPoint (added audio stream)
• Just in time
• Workshops (e.g. DigIR training)
• ASynchronous Distance Education

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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

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What do bioinformaticians need to knowAbstract
Skill Sets

• 1) 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.

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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.

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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.

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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

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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 TDWGs purview?
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Biological Informaticians Skill Set
e.g. UIUC, MS in Bioinformatics
Core Requirements
Computer Science
CS 411 Database Systems CS 473 Algorithms
Biology
18 to choose from
Bioinformatics
( computational biomolecular informatics) Applie
d Bioinformatics Bioinformatics Laboratory
Techniques in Bioinformatics Algorithms in
bioinformatics Principles of Systematics Computi
ng in Molecular Biology Genomics, Proteomics, and
Bioinformation
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Concentration / Disciplinary
Current Courses
New this Semester
Proposed
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

• Natural Science Ontologies
• Science Communication
• Biodiversity and Ecology Informatics

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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

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Educational Objects

• Education materials are type 3 documents.
• Need templates.
• Parts of educational objects
• Standard
• Dependencies
• Primer
• Demonstrations
• Exercises

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Synchronous Distance Ed
Internet
Student
VOIP Conference Skype
Classroom Instructor Students
TDWG Meeting
Student
Video/Desktop sharing Conference e.g.Webhuddle
Scientist