The data limbo in modern biomedical research Jorge Bouças
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The data limbo in modern
biomedical research
Jorge Bouças
Problem Resources Solution
¿ ✔ ︎
Problem Resources Solution
¿ ✔ ︎
The “bottom-up” / “top-down” paradigm
Pre-school
Universities Brazil
South Korea
Pre-school
Universities Brazil
South Korea
Bui
ld /
Con
stru
ct
Man
age
/ Dec
isio
n m
akin
g The “bottom-up” / “top-down” paradigm
Profit focused organizations
Knowledge, sharing, innovation
IT
Research
Production Biologics
Chemistry
Material Sciences
Knowledge, sharing, innovation
IT
Research
Production Biologics
Chemistry
Material Sciences
0 25 50
User generated input
Company’s website
News articles
Trust (%) March, 2014
Knowledge sharing
Organization structure
Information and Organization
Information and Organization
Structure-driven profit
Information-driven innovation
Information Technology
(IT) platforms
Information and Organization
Information Technology
(IT) platforms
machine human
Old concept
New interface
All-in-one
Simple!
User generated
content
Apps
Information and Organization
Information Technology
(IT) platforms Old concept
New interface
All-in-one
Simple!
User generated
content
Apps
machine human
Why start with labbooks?
Bot
tom
-Up
Electronic Laboratory Notebooks (ELNs)
Research
Planning Execution
Analysis
ELN
Electronic Laboratory Notebook
Index . . . . 12.08.2014 . RNA immuno-precipitation (RIP) . . .. ...
Apps App1 . . . . . Buffer App Add Serial Create Buffer . . . . AppX
Buffer Serial: B299, 22.07.2014
Quality by Design
Modified from Evernote
Free text + Apps
ELN + Laboratory Information Management System (LIMS)
Electronic Laboratory Notebooks (ELNs)
Research
Planning Execution
Analysis
ELN
Planning to Execution
Index . . . . 12.08.2014 . . . qPCR p21, GAPDH; Carcinomas . . .. ...
Apps App1 . . . . . . . . . . . . . . . . . qPCR 7600 Create Import files Analyze . . . . AppX
## qPCR p21, GAPDH; Carcinomas
Electronic Laboratory Notebook
Modified from Evernote
Planning to Execution
Settings.XML Results + info
Index . . . . 12.08.2014 . . . qPCR p21, GAPDH; Carcinomas . . .. ...
Apps App1 . . . . . . . . . . . . . . . . . qPCR 7600 Create Import files Analyze . . . . AppX
## qPCR p21, GAPDH; Carcinomas
Electronic Laboratory Notebook
Execution to Analysis
Results + info Settings.XML
## qPCR p21, GAPDH; Carcinomas
Planning, Execution, Analysis
Results + info Settings.XML
APPS
APPS
ELN
Execution to Analysis
Research
Planning Execution
Analysis
ELN
John
Anton Sylvia
Anna
Knowledge & Task Sharing
Research
Planning Execution
Analysis
John
Anton Sylvia
Anna
ELN
ELN
ELN
ELN
Information and Organization
Information Technology
(IT) platforms Old concept
New interface
All-in-one
Simple!
User generated
content
Apps
machine human
NLP ready!
Information and Organization
Information Technology
(IT) platforms Old concept
New interface
All-in-one
Simple!
User generated
content
Apps
machine human
1 Machine = 1 App
$$$
Training old
and
new personnel
$$$
Worldwide
deployment
Everybody can develop
and sell Apps
NLP ready!
Means and Ends
ü Implement a I&O platform
ü All sectors (Healthcare, Material Science…)
ü R&D based industry (Knowledge, tracking, SOPs-dependent)
ü All stages: from R&D to production
ü All levels: from technical staff to administration
✗ Sell software
Get work done for free!
1. Generate basis ELN + LIMS + Cloud solution package
2. Distribute package and source code for free
3. Keep control of official releases
ü Worldwide implementation (no extra costs)
ü Full control of roadmap
ü Reduce training costs of future employees (long term)
ü Free testing of new implementations
ü Increased feedback
ü Development of Apps and basic platform by third parties (Free + Commercial)
Find a partner!
Most popular!
Most popular!
Most popular!
Most popular!
Freeware + Commercial
Cloud, Storage, Communications
Databases, Big Data, Applications
Popular!
¿ ✔ ︎
Time (Year)
Com
putin
g P
ower
(R
elat
ive
Uni
ts)
Data science for machines
Time (Years)
Impa
ct fa
ctor
/ pa
per
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