Examples of three data management plans - (lib.stanford.edu ...

NSF Data Management Plan Notes from Professor Virginia Walbot, Biology, Oct. 2012.
The Plant Genome Research Program (PGRP) section of the biology directorate has required
a special appendix on data management since 1998, preceding the agency-wide requirement for a
data management plan. 5 pages are allowed for this section and two other items about
coordination among institutions. PGRP grantees do not file an item in FastLane in the usual
place for a data management plan. Other “special programs within NSF” also have particular
requirements in which applicants are instructed to NOT put an attachment in the FastLane data
management slot but to instead type in a code.
In my experience, a very short data management plan is preferable to a long one. I generally use
a larger font than in the proposal and make a table or list to be “perfectly” clear. These plans are
read by reviewers who appreciate brevity! If your proposal is recommended for funding, the
NSF program officers could ask you for more details. This only happened to me in 1998 when I
was asked to clarify if there would be a difference in distribution for non-profit and company
requests.
NSF Proposal PRGP 2007 Virginia Walbot (Stanford) and Zac Cande (UC-Berkeley)
Plant Genome Research Program (PGRP) The proposal was funded for 5 years at
approximately $1 M per year.
(A-1) Sharing of Results and Management of Intellectual Property
Sequence Deposit: All sequence data from this project will be deposited into GenBank at the
time of publication.
Community Resources: Cytological analysis including both photographs and written
descriptions of the male-sterile mutant collection will be deposited with the Maize Coop and
MaizeGDB approximately annually. Proteomics and transcriptome profiling data will be placed
in public databases at the time of publication. RT-PCR data that is not part of the supplementary
materials in publications will be available from the PI by FTP. This is the method by which we
delivered original DNA sequencing trace files to the community in the Maize Gene Discovery
Project.
PALM Instrument in the Bay Area. We realize that requesting a PALM for our study
is a very large investment of resources. Our plan to insure that this instrument benefits many
individual researchers in many labs is as follows. This instrument will be housed at Stanford
University to accomplish the two studies described in the proposal (fertile and mac1), and the
equipment will be available to the other 8 plant cell and molecular labs at the University and the
Carnegie Institution on campus. Several of these labs participated in the PALM demonstration
in summer 2005 and are eager to use the instrument; currently the closest instrument is at UC-
Davis, more than 100 miles away. In the second half of the project period, the PALM will be
moved to UC-Berkeley (most likely to be housed in the microscopy facility managed by Steve
Ruzin). The Cande lab will collect cells from additional mutants, and the ~20 plant cell and
development labs at UC-Berkeley and the PGEC will have access to the instrument.

Long-term Distribution: Clones, antibodies, and other resources will be distributed to public
sector users at the time of publication without any "reach through" restrictions on use. Modest
charges to cover shipping and handling may be assessed. Private sector user requests would be
evaluated by the Office of Technology Licensing at Stanford University (see below) prior to
distribution. All seed stocks in this project are already on deposit at the Maize Coop. For lines
of particular interest, double mutants and improved and expanded stocks will be constructed by
this research program. Such materials would be deposited at the Maize Coop at the time of
publication or by the end of the project for unpublished materials.
Intellectual Property: As described above the seed stocks, other materials, and data from this
project will be in the public domain, with free access to all. For some specialized biological
reagents, The Office of Technology Licensing at Stanford University promotes the distribution
of such materials from academic research into the private sector. Materials such as clones,
antibodies, and other biological reagents are typically distributed after payment of a one-time fee
($500 to $1000 per item). This fee is returned to the originating laboratory in a research account,
and the PI and coPI would decide how to spend such funds. Stanford University and UC-
Berkeley have a long history of cooperation in intellectual property issues. As part of the Maize
Gene Discovery Project the issues related to EST clones, transposon tagged genes and their
sequences, and maize genetics resources were thoroughly discussed in a meeting of the PI and
coPIs and the technology licensing departments of these institutions. As the lead institution,
Stanford will be responsible for coordinating and managing the intellectual property resulting
from this GEPR award.
2. NSF standard grant, Data Management Plan, 2011 Virginia Walbot PI
Policy on and Experience with Rapid Dissemination of Results. Stanford University
encourages rapid delivery of new data to public databases after editing, annotating, and
validation to meet community standards. The PI has extensive prior experience in this. For
example, during production of >200,000 maize ESTs in the Maize Gene Discovery Project, our
policy was to deposit trimmed data directly to GenBank in almost daily batches and then retrieve
it for analysis, putting us on an equal footing with others interested in maize ESTs in terms of
contig assembly, gene identification, etc. Similarly, during the Maize Full Length cDNA
Sequencing Project managed by the University of Arizona finished full length cDNAs were
released to GenBank in batches after the painstaking clone validation procedure, and these clones
were then simultaneously available for distribution at a nominal cost by the University of
Arizona. In both these projects individual community requests for additional information were
addressed within one or two days by V. Walbot, i.e. to send untrimmed sequence data, to provide
additional library information, to provide clones in advance (at a nominal cost), etc. In both
projects we also cooperated with individual investigator and large project requests for our
libraries, arrayed plates with cDNA or FLcDNAs plasmids in a timely manner. We recently
published (Pimentel et al. 2011) a method for displaying genetic records and family trees, and
made our own records the example (http://www.stanford.edu/~walbot/geneticrecords.html );
those requesting seed can look up from a computer or Smartphone all information about our
stocks and hence pinpoint precisely which stocks will work best for them. This tool has
increased our requests about five-fold in the past year.

MaizeGDB will be our primary portal for dissemination of results. A key early
decision in our current PGRP project was that we would not build a project website, but instead
rely on MaizeGDB for data dissemination. MaizeGDB uses us as an example of a model project
as we partially fund a specific employee (Dr, Lisa Harper, 50% FTE at MaizeGDB working from
the Plant Gene Expression Center, Albany CA) who participates in our PGRP project, is a coauthor
on papers to which she contributed, and is responsible for data entry into MaizeGDB
including cytological image evidence of hundreds of male-sterile lines. For the Maize-Ustilago
project the volume and complexity of data are much lower, and data deposit into MaizeGDB will
be performed by the PI and postdoctoral fellows. The following data types are anticipated:
Table 1. Data types from this project and how they will be disseminated.
http://www.stanford.edu/~walbot/ = lab website
http://www.stanford.edu/~walbot/geneticrecords.html = genetic records
Data type Where Deposited When # By Whom
Microarray & RNA- Track at Maize GDB Within 3 months of PI
Seq
and GEO
data validation by
qRT-PCR
Small protein Track at Maize GDB Within 3 months of PI
proteomes
data validation
Availability and use Posters, publications, When we have PI and Research team
of FRET sensors in and lab website validated use with a
transgenic maize
robust scientific study
Phenotypic data on Posters, publications, Publications PI and Research team
Ustilago-maize
interaction
and lab website
Ustilago gene cloning Posters and
After publication Gunther Doehlemann
and allele analysis publications
distributes Ustilago
stocks
Availability and use Posters, publications,
PI in collaboration
of endoscopes and lab website
with Mark Schnitzer
3. NSF Proposal (~$4.4 M for four years, 3 years funded plus 1 year extension) from the
PGRP.
Yeisoo Yu, PI University of Arizona, Cari Soderlund coPI of Arizona, Virginia Walbot coPI
Stanford Plant Genome Research Program 2004 - 2007
A-1. Sharing of Results and Management of Intellectual Property
Maize Full-length cDNA Project
A-1.1 It is our explicit intention that all data derived from this project be placed in public
databases as soon as produced and quality checked as outlined in the project description.
Specifically:
1) All single-pass cDNA sequences will be deposited in dbEST Genbank at weekly

intervals.
2) All finished FL-cDNA sequences will be deposited in dbEST Genbank.
3) cDNA clones produced from this proposal will be made publicly available from Arizona
Genomics Institute (AGI) BAC/EST Resource Center in University of Arizona.
4) High-density filter arrays of the full-length cDNA set will be available to the community
through the AGI BAC/EST Resource Center.
5) Aliquots of amplified cDNA libaries 1 and 2.
There are no IP issues (restrictions) related to the use of any of the materials.
A-1.2 Making the public aware of our new resources. Public awareness of the resources will
be through, AGI and Stanford websites, as well as collaborative web links from Gramene and
MaizeGDB databases to our database and AGI webbased ordering system
(http://genome.arizona.edu/orders) for accurate and easy clone identification and distribution.
We will provide community awareness of our resources produced at scientific conferences, from
emails and direct conversations.
A-1.3 All clone distribution will be handled through the AGI BAC/EST Resource Center.
Distribution of resources requiring protection of Intellectual Property is handled by a community
member’s institution providing a signed standard Universal Biological Material Transfer
Agreement (UBMTA). An example of the AGI MTA is available at AGI web ordering system
(http://www.genome.arizona.edu/orders/).
A-1.4 Fees charged by the AGI BAC/EST Resource Center for resources are based on cost
recovery and take into account the cost of all reagents, labor, shipping, service contracts and
instrument depreciation. The pricing structure is as follows:
Pricing to academic institutions Pricing to for profit companies
• Library $12.00/plate plus shipping $50.00/plate plus shipping
• Clones $6.00/clone plus shipping $30.00/clone plus shipping
• High-density filter arrays $150.00/filter plus shipping $250.00/filter plus shipping
• Amplified Library $250.00/1ml aliquot of amplified library. Not available until the end
of the project