Training Material for iPG2P Team Members (DRAFT)
Jeff White, USDA ARS and Chris Myers, 15 Sept. 2009
The iPlant Genotype to Phenotype initiative (“iPG2P”) faces serious challenges in ensuring that
researchers from diverse disciplines work together effectively. Software development presents especially
challenging cases of interdisciplinary projects and that their high failure rates (The Standish Group, 1999)
often relate to team members having a poor understanding of one another’s capabilities, needs and
expectations (McConnell, 1996). Open source software development can alleviate certain constraints
related to communication but is not a panacea (Fogel, 2005).
In the Sept. 8 iPG2P teleconference, the steering committee recommended that we develop a
strategy for making available basic training to team members, recognizing that resources (especially time)
are limited and that the training needs vary greatly among our membership. A normal part of the research
process is to conduct background reading and study to learn new techniques or to gain insights and
knowledge. There is a vague, partially valid assumption that researchers are sufficiently motivated to
identify gaps in their personal knowledge, differentiating between what might be interesting to know and
what is essential for the research at hand. Given our limited resources both of time and funding, we need
to find the balance between training and moving ahead with our work.
Five options that appear viable are individual mentoring and instruction, self-guided study, online tutorials, training sessions in workshops (or as stand-alone activities), and short courses.
Individual mentoring and instruction
Members of iPG2P who host the iPlant post-doctoral fellows will provide the basic guidance and
orientation normally afforded visiting scientists.
Self-guided study
A normal part of the research process is conduct background reading to learn new techniques or
gain insights and knowledge. Presumably, participating researchers are sufficiently motivated to identify
major knowledge gaps, so the challenge is to connect researchers with quality resources. Additionally,
iPG2P might identify people willing to suggest additional reading or answer questions. Table 1 provides
examples of annotated lists of reading materials and other resources. This material should eventually be
managed through the iPG2P web site.
On-line Tutorials
On-line tutorials can provide more structure than self-guided study. iPlant might want to survey
existing training programs. The CGIAR’s Generation Challenge Program has material for bioinformatics
and related topics (e.g.,
http://mcclintock.generationcp.org/index.php?option=com_content&task=section&id=19&Itemid=170).
For specific activities such as use of software tools, an especially valuable resource is demonstration
videos. Good examples are found at http://showmedo.com/videotutorials/, which hosts short videos on
how use of diverse open source tools.
Workshop training sessions
If time allows, training sessions might be incorporated into workshops or annexed to workshops.
Presumably, as iPG2P starts generating software tools, we will assess the tools and this will require some
training activities.
Short courses
There are numerous short courses that might prove useful to individuals. Examples are provided
in Table 2. While useful, the costs and time commitments appear higher than for the other alternatives.
References
Fogel, K. 2005. Producing Open Source Software. http://producingoss.com/
McConnell, S. 1996. Rapid Development. Edited by . Redmond, WA: Microsoft Press.
Standish Group. 1999. CHAOS: A recipe for success. www.standishgroup.com
Table 1. Examples of references and accompanying text for self-guided study. The resource person serves
as a point of contact for questions or additional instructional material within iPG2P.
Resource
Reference and comments
person
Genetics and Molecular Biology
Basic Genetics and Molecular Biology
Robinson, T.R. 2009. Genetics For Dummies. Wiley, John & Sons. (Paperback, $14)
Claverie, J. and C. Notredame. 2003. Bioinformatics for Dummies. Wiley, John & Sons.
(Paperback, $14)
Statistical Inference
Mixed Modeling
Galwey, N. W. 2006. Introduction to Mixed Modelling: Beyond Regression and Analysis of
Variance. Chichester, UK: John Wiley & Sons.
Introduces mixed modeling for people having basic familiarity with ANOVA and regression.
Examples given using Genstat and R, but downloadable files include SAS code.
Association mapping
Balding, D. J. 2006. A tutorial on statistical methods for population association studies. Nature
Reviews Genetics. 7(10):781-791.
Modeling of Biological Systems
Ecophysiological Modeling
Hay, R. and J. Porter. 2006. The Physiology of Crop Yield. Second ed. Oxford, UK: Blackwell
Publishing. (Paperback, $72).
Jeff
White
Presents whole plant physiology using process-based modeling as a framework for much of the
discussion. Assumes basic undergraduate biology background. Chapter 2 is a good overview of
modeling phenology. Weak on stress physiology.
Loomis, R.S., R. Rabbinge, and E. Ng. 1979. Explanatory models in crop physiology. Annual
Review of Plant Physiology 30:339-367.
Landmark review of the role simulation modeling in plant physiology.
Jeff
White
Systems Biology Markup Language (SBML)
Laisk, Nedbal and Govindjee (eds.). 2009. Photosynthesis in silico: Understanding Complexity
from Molecules to Ecosystems. ($279.00).
Chris
Myers
Overview of modeling of photosynthetic processes at different scales of resolution (special
issue of "Advances in Photosynthesis and Respiration")
http://www.springerlink.com/content/978-1-4020-9236-7
Hucka and Schaff . 2009. Trends and tools for modeling in modern. In Laisk, Nedbal and
Govindjee (eds.). 2009. Photosynthesis in silico: Understanding Complexity from
Chris
Myers
Molecules to Ecosystems.
This chapter deals specifically with SBML.
http://www.springerlink.com/content/l275432j6p7262jj/?p=51a7bb7e82224b15bb6b6ec53b06e
8d4&pi=0
www.sbml.org
General portal for SBML resources.
Visualization
Basic design and philosophy
Tufte, E.R. 1983. The Visual Display of Quantitative Information. Graphics Press. Chelshire,
Connecticut.
Tufte is a long time crusader for clarity and simplicity in presenting data. “He writes, designs,
and self-publishes his books on analytical design, which have received more than 40 awards for
content and design. He is Professor Emeritus at Yale University, where he taught courses in
statistical evidence, information design, and interface design. His current work includes
landscape sculpture, printmaking, video and a new book. (www.edwardtufte.com)
Software Development
Open Source Software
Fogel, K. 2005. Producing Open Source Software. http://producingoss.com/
Excellent background information for anyone working on open source projects. Emphasizes
human interactions. No programming knowledge required.
Raymond, E. 2000. The Cathedral and the Bazaar. http://www.catb.org/~esr/writings/cathedralbazaar/cathedral-bazaar/
Seminal paper on why open source development works.
Chris
Myers
ShowMeDo web site of online videos. http://showmedo.com/videotutorials/
Has short demonstrations for numerous programming languages including Python, Java and
Perl.
Table 2. Short courses of potential interest to iPG2P members.
Assessing Crop Production, Nutrient Management, Climatic Risk and Environmental Sustainability with
Simulation Models.
May 10 - 19, 2010, Griffin, GA. http://www.icasa.net/events/dssat2010.html
Cost: $1200 (?) plus lodging and dining (breakfast and lunch are provided).
Introduction to application of ecophysiological modeling. Very “hands on” with individual instruction
so suitable for a broad range of backgrounds. Emphasizes DSSAT software. Jeff White is an
instructor. Repeated every two years. Occasionally given in modified form elsewhere.
Molecular Plant Breeding - An International Short Course on Practical Applications of Molecular tools
for Plant Breeding
Aug. 29—Sept. 3, 2010. http://www.worldtap.msu.edu/home/page/70
“This course in Molecular Breeding will be designed not only to cover the molecular techniques
available to a plant breeder for crop improvement but also to cover marker assisted selection with
successful examples from around the world. In addition, this course will introduce the participants on
how to develop international collaborations in plant breeding and approach funding opportunities
nationally, regionally and internationally.”
Cold Spring Harbor Laboratory – Check their web site for diverse listings.
http://meetings.cshl.edu/courses.html