Award Abstract # 1440323
EarthCube Building Blocks: Collaborative Proposal: GeoSoft: Collaborative Open Source Software Sharing for Geosciences

NSF Org: RISE
Integrative and Collaborative Education and Research (ICER)
Recipient: UNIVERSITY OF SOUTHERN CALIFORNIA
Initial Amendment Date: August 14, 2014
Latest Amendment Date: August 14, 2014
Award Number: 1440323
Award Instrument: Standard Grant
Program Manager: Eva Zanzerkia
RISE
 Integrative and Collaborative Education and Research (ICER)
GEO
 Directorate for Geosciences
Start Date: September 1, 2014
End Date: August 31, 2018 (Estimated)
Total Intended Award Amount: $1,048,000.00
Total Awarded Amount to Date: $1,048,000.00
Funds Obligated to Date: FY 2014 = $1,048,000.00
History of Investigator:
  • Yolanda Gil (Principal Investigator)
    gil@isi.edu
  • Chris Mattmann (Co-Principal Investigator)
Recipient Sponsored Research Office: University of Southern California
3720 S FLOWER ST FL 3
LOS ANGELES
CA  US  90033
(213)740-7762
Sponsor Congressional District: 34
Primary Place of Performance: USC-Information Sciences Institute
4676 Admiralty Way, Suite 1001
Marina del Rey
CA  US  90292-6611
Primary Place of Performance
Congressional District:
36
Unique Entity Identifier (UEI): G88KLJR3KYT5
Parent UEI:
NSF Program(s): EarthCube
Primary Program Source: 01001415DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 7433
Program Element Code(s): 807400
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.050

ABSTRACT

Geosciences software embodies crucial scientific knowledge, and as such it should be explicitly captured, curated, managed, and disseminated. The goal of this project is to create a system for software stewardship in geosciences that will empower scientists to manage their software as valuable scientific assets. Scientific software stewardship requires a combination of cyberinfrastructure, social infrastructure, and professional development infrastructure. The framework will result in an open transparent and broader access to scientific software to other scientists, software professionals, students, and decision makers. It will significantly improve the adoption of open data and open software initiatives, improve reproducibility, and advance scientific scholarship.

The proposed research will advance knowledge and understanding of scientific software as a valuable community asset that is worth sharing, curating, cataloging, validating, reusing, and maintaining.
1) Facilitating software publication through TurboSoft, a personal assistant (analogous to TurboTax) that guides a user through best practices. Users will choose the degree of investment they are willing to make in componentizing, describing, licensing, and maintaining their software. The system will encourage open source publication, the formation of communities around the software, and set up mechanisms for software citation and credit.
2) Enabling broad software dissemination through GeoSoft, a "software commons" for geosciences that will support software contributions (prepared through TurboSoft or otherwise), software discovery through multi-faceted search, and foster social interactions through dynamic formation of communities of interest. GeoSoft will interoperate with existing software repositories and modeling frameworks in geosciences.
3) Providing just-in-time training materials through GeoCamp, an annotated collection of educational units ranging from basic education to professional training on all aspects of software stewardship. GeoCamp will be seamlessly integrated with TurboSoft and GeoSoft, and present a wide range of options for learning in the context of a user?s context of interaction with the framework or independently.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 23)
Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schoberhidden "FAIR Computational Workflows" Data Intelligence , v.2 , 2019 10.1162/dint_a_00033
Christina L Zheng, Varun Ratnakar, Yolanda Gil, and Shannon K McWeeney "Use of Semantic Workflows to Enhance Transparency and Reproducibility in Clinical Omics" Genome Medicine , v.7 , 2015 10.1186/s13073-015-0202-y
Daniel Garijo and Maximiliano Osorio and Deborah Khider and Varun Ratnakar and Yolanda Gil "OKG-Soft: An Open Knowledge Graph with Machine Readable Scientific Software Metadata" Proceedings of the Fifteenth International IEEE eScience Conference , 2019 10.1109/eScience.2019.00046
Daniel Garijo, Yolanda Gil, Oscar Corcho "Abstract, Link, Publish, Exploit: An End to End Framework for Workflow Sharing" Future Generation Computer Systems, Volume 75, October 2017. , v.75 , 2017
Gil, Y.; Ratnakar, V.; and Garijo, D "OntoSoft: Capturing Scientific Software Metadata" Proceedings of the Eighth ACM International Conference on Knowledge Capture , 2015 10.1145/2815833.2816955
Lucas Carvalho and Daniel Garijo and Claudia Bauzer Medeiros and Yolanda Gil "Semantic Software Metadata for Workflow Exploration and Evolution" Proceedings of the Fourteenth IEEE International Conference on eScience , 2018 10.1109/eScience.2018.00132
Matty Mookerjee and Daniel Vieira and Marjorie A. Chan and Yolanda Gil and Terry L. Pavlis and Frank S. Spear and Basil Tikoff "Field Data Management: Integrating Cyberscience and Geoscience" Earth and Space Science News , 2015 http://dx.doi.org/10.1029/2015EO036703
Odd Erik Gundersen, Yolanda Gil, David W. Aha "On Reproducible AI: Towards Reproducible Research, Open Science, and Digital Scholarship in AI Publications" AI Magazine , v.39 , 2018 10.1609/aimag.v39i3.2816
Ricky J. Sethi and Yolanda Gil "Reproducibility in Computer Vision: Towards Open Publication of Image Analysis Experiments as Semantic Workflows" Proceedings of the Twelfth IEEE Conference on eScience , 2016 10.1109/eScience.2016.7870918
Ricky J. Sethi and Yolanda Gil "Scientific Workflows in Data Analysis: Bridging Expertise Across Multiple Domains" Future Generation Computer Systems , v.75 , 2017 10.1016/j.future.2017.01.001
Xuan Yu, Chris Duffy, Yolanda Gil, Lorne Leonard, Gopal Bhatt, and Evan Thomas "Cyber-Innovated Watershed Research at the Shale Hills Critical Zone Observatory" IEEE Systems Journal , v.10 , 2016 10.1109/JSYST.2015.2484219
(Showing: 1 - 10 of 23)

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

Geosciences software embodies crucial scientific knowledge, and as such it should be explicitly captured, managed, and disseminated. The goal of this project was to improve software stewardship in geosciences by empowering scientists to manage their software as valuable scientific assets. Scientific software stewardship requires a combination of cyberinfrastructure, social infrastructure, and professional development infrastructure. Software stewardship practices give open transparent and broader access to scientific software to other scientists, software professionals, students, and decision makers.

In this project we developed OntoSoft, a framework for cataloguing of scientific software that follows best practices for open software sharing and reuse.  OntoSoft is a federated catalog, so each scientific community can maintain its own repository but all repositories are interconnected.  OntoSoft includes a distributed query system to enable users to find software across different OntoSoft repositories.  OntoSoft allows crowdsourcing of software metadata by incorporating an access control system in OntoSoft so users can control who can edit the metadata about their software.

To improve awareness and train scientists to improve software dissemination, this project also resulted in the Geoscience Papers of the Future (GPF) Initiative.  This initiative, initially developed by the 30+ members of OntoSoft’s Early Career Advisory Committee, produced training materials that were used in dozens of training sessions that involved hundreds of geoscientists.  These sessions were held at conferences, universities, and government laboratories.  The sessions teach scientists to write papers that incorporate best practices of open source data and software sharing, reproducible publications, and digital scholarship. We refer to these papers as Geoscience Papers of the Future. A Special Issue of the American Geophysical Union’s Earth and Space Science journal included a collection of such papers.  The initiative had particularly strong uptake in the geospace sciences community, which studies the interactions between the Earth’s upper atmosphere with interplanetary space.  A broader follow up of this initiative was the Scientific Paper of the Future initiative, with participation from neuroscience and more recently the artificial intelligence communities.

More details about the project can be found at https://www.ontosoft.org/.


Last Modified: 06/15/2020
Modified by: Yolanda Gil

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