Transcript Crux-Final_Demo_Slideshow

Crux
flexible, structured data reporting
for funding agencies
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
* From MJFF Website
most affected in Parkinson’s disease …’ *
What is the data supporting this claim?
Current state-of-the-art
‘Data Sharing’
File sharing systems
provide centralized,
secure access to files
But this is ‘just’ a
complex shared*
directory.
How to keep track of
the science easily
and efficiently?
The https://brainfu.org site
* with apologies to the brainfu
designers.
Capturing Scientific
Communication
•
Two primary areas of
communication breakdown
1. Experimental
Procedures
2. Experimental Data
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
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 Files
•
Lab Notebooks,
Computer Files, Images,
Spreadsheets, Text
Documents, etc.
•
Sometimes imported
into ad-hoc summary
databases
•
Data decoupled from
experimental procedure
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?
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.
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.
This presentation
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
1.
How it Works – A
Walkthrough
a demonstration of experiment management with crux
*image by webtreats
1. Dashboard
•
Serves as a focal
point summarizing
the contents of the
system
•
Each experiment
listed separately
•
Links to:
-
metadata
-
design
-
data
2. Experimental Design
•
The Experimental
Design Diagram
•
Protocol
represented as a
diagram
•
Clear complete
description of the
experiment
From Experimental Design
to Data Design
Dependency between measurements and
parameters is provided by tracing backwards
through the protocol.
Codman in-vivo
Note that model
is not complete,
but works well for
simple
measurements +
analysis
Simple Data Gathering
•
Low burden on
the investigator
•
Spreadsheets
used as the data
forms
•
Files and images
are uploaded into
Crux with the data
Experiments in the demo
Experiments in
system:
•
Codman
- in-vitro
- in-vivo
•
Emborg
- in-vitro
- ex-vivo
- in-vivo
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 professionallycurated terms with
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
A Complete Solution
•
Clear evolvable
experimental descriptions
•
Automatic database
creation
•
Data import through
spreadsheets
•
Data query, report and
export
Describe
Gather
Query
Demo Walkthrough –
From Design to Data
SYSTEM
DEMONSTRATION
Demo Walkthrough –
Application Flow
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.
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
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 welldeveloped 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
Thank You
*image by wasabicube