Alex Kuhn (of the University of Illinois) instructs Patty Kaishian (of Syracuse University) on how to enter label data from microfungi specimens. Their work is part of the Microfungi Collections Consortium, funded through the ADBC program. Credit: Andrew N. Miller, Illinois Natural History Survey, University of Illinois
By Deborah Paul for iDigBio and Data Carpentry
Keywords: Data Carpentry, Gordon and Betty Moore Foundation, Biodiversity informatics skills, Reproducible research
Re: In support of 21st century biodiversity informatics skills and tools for reproducible research
Information Contact: info@datacarpentry.org
We’re happy to share news from Data Carpentry (DC) (http://datacarpentry.github.io/). The Gordon and Betty Moore Foundation just agreed to DC’s grant proposal for funds to support staff and expand the reach of Data Carpentry and the development of more DC materials (https://github.com/datacarpentry).
[referenced from a prior blog post] From the COLLAB-IT* meeting in September of 2013, one break-out group coalesced an idea into action to form Data Carpentry. The IT groups from NESCent, BEACON, iDigBio, NEON, iPlant, SESYNC, DataONE, and NIMBios shared their observations about data literacy and computational literacy skills needs across the stakeholders in these overlapping communities. Course content needed to address these skills gaps make up the Data Carpentry curriculum.
Following the Software Carpentry (http://software-carpentry.org) (SC) model, Data Carpentry seeks to improve and enhance researchers skills needed to collect, manage, and analyze data efficiently. We aim to teach skills that result in reproducible, sustainable scientific workflows that result in discoverable, re-useable datasets and reproducible analysis.
iDigBio team members (Matt Collins, Deb Paul, Kevin Love, Libby Ellwood) are actively involved in the DC and SC communities. You can join us too! Find out how at http://datacarpentry.github.io/. We’ve been using DC materials in our iDigBio workshops, and we are developing enhanced modules that focus on collections data use, re-use, visualization, analysis, and management. Some TCN and USGS members are participating as well including Katja Seltmann (TTD-TCN) and Derek Masaki (USGS-BISON).
We look forward to the opportunities this new funding will make possible. Thank you Moore Foundation for helping us addre
ss biodiversity informatics skills needs across our diverse communities.
Please let us know your thoughts. What skills do you need? What else do we need to cover? Got an idea for where to host one of these? Thanks for reading and stay tuned for more Data Carpentry!
Grant details: The DC Moore Foundation Grant Proposal is up on Figshare.
*Collaborative-IT (COLLAB-IT) is a group supported by funds from NSF through the SESYNC project. COLLAB-IT meets at least once-a-year. Members are from the IT staff across the NSF BioCenters including: BEACON, iPlant, DataONE, NIMBios, SESYNC, NESCent, NEON, and iDigBio. Our goals are to find overlapping synergies where we can work collaboratively toward meeting common/shared needs in our broader scientific communities.
"The localities and dates of collection associated with these vouchered specimens provide the only large-scale, verifiable data available on native distributions of organisms and how those distributions have changed over time."
On July 26, 2015, iDigBio hosted an all-day ecological niche modeling (ENM) workshop at Botany 2015, the joint annual conference hosted by the Botanical Society of America, Plant Canada, and their affiliated societies, in Edmonton, Alberta.
June 29, 2015
By Dr Shelley James
Backed by Denny Luan, Tracie Mackenzie, Amy Collette, Nikki & Friends, Elise & Tiffy, Bo Sprotte Kofod, John B. Hall, David Esopi, Donna Robbins, Pureum Kim, Robert Whitton, and Perth Friends
About This Project
The Solomon Islands archipelago in the Pacific Ocean has an estimated plant diversity of 4500 species, the same diversity as Texas, but on only 4% of the land area. Intensive biodiversity surveys are urgently needed in this remote location as many new species await discovery. This project will rapidly assess the flora of the highest peaks of Guadalcanal and develop conservation plans to protect against deforestation and invasion of non-native species threatening this unique floral biodiversity.
What is the context of this research?
Few botanical specimens have been collected from the upper elevations of Guadalcanal. For example, Bishop Museum has only about 800 botanical specimens from the island, and none are from the high, biologically diverse mountain tops. Intensive surveys are expected to result in the discovery of many new species and the documentation of new populations of rare species.
Collecting new specimens will enable scientists and Solomon Islanders to better understand the floral biodiversity and distribution of plants on Guadalcanal in order to develop conservation plans for the region. I have been developing an up-to-date species list of the flora of the Solomon Islands, and new botanical surveys will help validate this already gathered data.
What is the significance of this project?
The rainforests of the Solomon Islands are listed on the World Wildlife Fund's (WWF) Terrestrial Ecoregions of conservation priority. The flora and fauna of the archipelago are considered to be vulnerable due to the clearing of forest for tropical timber, large-scale agricultural plantations and subsistence gardening, largely as a result of population growth. The native forest is also increasingly threatened by non-native species that invade the diverse native forests.
Climate change is expected to influence the diversity of the region, but a baseline measure of the flora in the mountains is needed to gauge these effects into the future. Collections made will also provide needed specimens for other botanical researchers around the world unable to travel to this remote region.
What are the goals of the project?
Working with a team of scientists from around the globe, and with your support, I will survey the intact forest of the high-elevation interior of Guadalcanal for ca. 20 days in September, 2015. Each flowering and fruiting plant specimen will be photographed and collected to document the diversity of species in each area surveyed. Pieces of tissue will also be sampled and preserved for molecular research projects. Specimens resulting from this expedition (>1,000 specimens) will significantly enhance the understanding of the floral biodiversity of Guadalcanal. The distribution and density of endangered, rare and threatened species, and invasive species will be documented. The project will also involve the training of at least one Solomon Islander in biodiversity assessments.
To help fund this exciting expedition go to the original announcement!
iDigBio API Hackathon Report Blog
Plantingscience.org is now accepting applications for the 2015-2016 Master Plant Science Team.Apply by August 21, 2015Are you a graduate student or post-doctoral researcher interested in a chance to get involved and trained in K-12 outreach? Would you like to mentor student research teams, without ever leaving your desk? Do you have the time to commit to mentor ~4 teams in both the Fall and Spring PlantingScience Sessions? Discover the rewards:
What are the expectations of the Master Plant Science Team members?
Interested members of the Master Plant Science Team may also participate in field-testing of new curricular modules, shadowing student experiments, communicating with teachers and module authors, and providing feedback on module materials and development. Sponsorship is provided by the following partner societies:
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Laura Maihofer, electronic imaging technician, imaging the specimen note cards of Edwin B. Mains, who was a prominent mycologist at U-M who served as director of the Herbarium, president of the Mycological Society of America, and described many new fungi among other achievements. Image credit: Matthew Foltz.
