1. Crux flexible, structured data reporting for funding agencies

2. The Challenge MJFF has a comprehensive, large-scale funding program (~40 programs, ~680 funded projects) Final reports are written documents, summarized as abstracts. e.g., Prochaintz & Harmann (Fast track 2007): ‘… the protein Engrailed is able to rescue the neurons most affected in Parkinson’s disease …’ * What is the data supporting this claim? * From MJFF Website

3. Current state-of-the-art ‘Data Sharing’ File sharing systems provide centralized, secure access to files But this is ‘just’ a complex shared directory. The https://brainfu.org site * with apologies to the brainfu designers. * How to keep track of the science easily and efficiently?

4. Capturing Scientific Communication Two primary areas of communication breakdown 1. Experimental Procedures 2. Experimental Data

5. Experimental Procedures Poorly described at the beginning (grant proposal) and end of the process (publication) Difficult to replicate experiments Difficult to design the next experimental step Difficult to track changes

6. Experimental Data Only summary data available during grant assessment and after publication Difficult to evaluate progress during grant assessments Greatly diminishes utility of meta-analysis Results are decoupled from the supporting raw data

7. Data Files Lab Notebooks, Computer Files, Images, Spreadsheets, Text Documents, etc. Sometimes imported into ad-hoc summary databases Data decoupled from experimental procedure

8. Inconsistency + Evolution Over the course of any project: Procedures and data formats may change Original requirements may change or be refined Data schema will be updated to reflect this but what happens to data in previous versions of the database?

9. Why? Why is this happening? Capturing and communicating this information using currently available methods is burdensome and haphazard. Why is this a problem? Too much critical data stays in the researcher’s head and private notebooks.

10. What Is Crux? A user friendly tool to record all critical data at point of funding and throughout the course of research. Use standard terminology to describe data - Precise curation using community bio-ontologies Formats are easily understood by scientists and Funders Data, procedures, and experiment designs are permanently linked and stored in a unified file system.

11. Benefits All data is preserved (including negative results and failed procedures) All data is held by Funders Data sharing contract agreements are simplified: (e.g., Experiment design and data will be deposited in Crux at quarterly intervals” Reviewers have access to raw data Data could ultimately be shared with the research community

12. User Friendly Graphical design of each experiment procedure creates a custom data repository Facilitated with professional curation All data can be viewed in the context of the full design

13. This presentation 1. Walkthrough a. Crux web-application b. Experimental design tool c. OBI ontology curation d. Designs and experimental data for Emborg + Codman e. Upload / download of data using spreadsheets 2. Demonstration a. Enter a new experimental design LIVE! 3. Overview of workload associated with model construction, data entry and ontology curation 4. Overall Accomplishments 5. Preliminary description of plans for year 2

14. How it Works – A Walkthrough a demonstration of experiment management with crux *image by webtreatswebtreats

15. 1. Dashboard Serves as a focal point summarizing the contents of the system Each experiment listed separately Links to: - metadata - design - data

16. 2. Experimental Design The Experimental Design Diagram Protocol represented as a diagram Clear complete description of the experiment

17. From Experimental Design to Data Design Codman in-vivo Dependency between measurements and parameters is provided by tracing backwards through the protocol. Note that model is not complete, but works well for simple measurements + analysis

18. Simple Data Gathering Low burden on the investigator Spreadsheets used as the data forms Files and images are uploaded into Crux with the data

19. Experiments in the demo Experiments in system: Codman - in-vitro - in-vivo Emborg - in-vitro - ex-vivo - in-vivo

20. Standardized Terminology Professional curation produces accurate and clearly understandable experiment designs Using NIH-funded community repositories of curation terms enables data mining and sharing Crux allows a curator to associate professionally- curated terms with experimental elements

21. Curation In Parallel Reviewers and Investigators are not burdened by the curation process The system gets more and more useful as the curation gets more detailed

22. A Complete Solution Clear evolvable experimental descriptions Automatic database creation Data import through spreadsheets Data query, report and export Describe Gather Query

23. Demo Walkthrough – From Design to Data SYSTEM DEMONSTRATION

24. Demo Walkthrough – Application Flow

25. M.J.F.F. Programs Experimental Programs: Discovery / Translational / Clinical / (+ some I.T. development, such as this project). The long-term objective of this system is to enable any scientist in an executive role (program officers, journal editors, foundation executives) to do more than address the question: ‘were the goals of the project fulfilled?’ We want to provide data management, sharing and analysis so that these individuals can guide and accelerate research by (a) gaining access to all the data (b) performing meta-analysis and knowledge synthesis over that data.

26. Further Development The 2010 system was funded as a proof-of-concept prototype Future funding targets Beta software for use at MJFF, the Kinetics Foundation and other agencies if possible Developers will work closely with beta testers in MJFF and The Kinetics Foundation Crux will also be developed and distributed as a capability within the Biomedical Informatics Research Network (BIRN, http://www.birncommunity.org/), a community organization building infrastructure for the biomedical community.http://www.birncommunity.org/

27. Year 2 Plans Development of a system tailored to manage a well-specified set of grants pertaining to a family of experiments conforming to a well- developed experimental design (i.e. infusion studies) ‘Dashboard’ display will form central focal point and be based on a summary of designs, evolution of these designs and the presence of data within them Proposed additional features will include: - data visualization - structured coordination with professional curators - inter-experiment querying

28. Thank You *image by wasabicubewasabicube