Software Engineers are the Priests of the Modern Age,

1
Applied Interactional Expertise in Scientific
Trading Zones
Software Engineers are the Priests of the Modern
Age,
A mysterious cult standing between The People and
Reality.
This situation is unacceptable,
Especially in science, the nominated interpreter
of reality!
2
The Problem
Software Engineers are the Priests of the Modern
Age,
A mysterious cult standing between The People and
Reality.
This situation is unacceptable,
Especially in science, the nominated interpreter
of reality!
Dumb idea 0
Software engineers must become scientists,
So they can be contributory experts in these
fields.
The only way to do this,
Is to teach software engineers to be molecular
biologists.
3
(No Transcript)
4
The Problem
Software Engineers are the Priests of the Modern
Age,
A mysterious cult standing between The People and
Reality.
This situation is unacceptable,
Especially in science, the nominated interpreter
of reality!
Dumb idea 0
Wrong!
Software engineers must become scientists,
So they can be contribitory experts in these
fields.
The only way to do this,
Is to teach software engineers to be molecular
biologists.
5
The Problem
Software Engineers are the Priests of the Modern
Age,
A mysterious cult standing between The People and
Reality.
This situation is unacceptable,
Especially in science, the nominated interpreter
of reality!
Dumb idea 1
We need artificial intelligence,
So computers can be contributory experts in these
fields.
The only way to do this,
Is to teach computers to be molecular biologists.
6
Afferent helps chemists do drug discovery.
Afferents goals Close the synthetic/analytic
loop on drug (lead) discovery. Give scientists
direct control over the discovery process.
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Chemists Teach Afferent Organic Chemistry
8
Afferent Runs Chemical Robots to Do the Reactions
9
Afferent Simulates the Chemistry
10
Afferent can see both successes and failures in
mass spec data.
11
Afferent can make educated guesses about what
might have gone wrong
12
Afferent helps chemists do drug discovery.
Afferents goals Close the synthetic/analytic
loop on drug (lead) discovery. Give scientists
direct control over the discovery process.
Afferents successes Close the
synthetic/analytic loop on drug (lead) discovery.
Afferents failures Scientists felt like they
had less control.
13
The Problem
Software Engineers are the Priests of the Modern
Age,
A mysterious cult standing between The People and
Reality.
This situation is unacceptable,
Especially in science, the nominated interpreter
of reality!
Dumb idea 1
Wrong!
We need artificial intelligence,
So computers can be contributory experts in these
fields.
The only way to do this,
Is to teach computers to be molecular biologists.
14
What laboratory life is REALLY like (for a
computer scientist)
15
The Problem
Software Engineers are the Priests of the Modern
Age,
A mysterious cult standing between The People and
Reality.
This situation is unacceptable,
Especially in science, the nominated interpreter
of reality!
Dumb idea 2
We need a New Enlightenment,
Where scientists directly control computation.
The only way to do this,
Is to teach scientists to program and let them do
it.
16
BioBike enables biocomputation for molecular
biologists.
BioBikes goals Give scientists direct control
over the discovery process. Provide access to
all the desired biological knowledge. Let the
scientists actually do the programming. Embed
biocomputing in a collaborative community of
biologists working together on problems.
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What biologists want to do
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The state-of-the-art in Bioinformatics an
infinitude of one-off hacks to integrate
knowledge from almost redundant, slightly broken,
giant, remote knowledge bases.
PERL
XYZZY
Python
Corba
FTP FASTA
XML
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Web Based Listener
Object Persistence
Security v. Collaboration
KnowOS
Process Management
Efficient Scripting
Integrated Knowledge
Toolset Integration
Ability to read Upside Down
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Knowledge Operating System integrates knowledge
resources
KnowOS Integrated Knowledge Server
Biocomputational Tools and Sims
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Dotty output
Call Dotty
Call Phylip
Call Clustal
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Teach scientists to program
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BioBike enables biocomputation for molecular
biologists.
BioBikes goals Give scientists direct control
over the discovery process. Provide access to
all the desired biological knowledge. Let the
scientists actually do the programming. Embed
biocomputing in a collaborative community of
biologists working together on problems.
BioBikes successes Knowledge OS does offer
unprecedented integration.
BioBikes failures The scientists didnt
actually do the programming!
24
The Problem
Software Engineers are the Priests of the Modern
Age,
A mysterious cult standing between The People and
Reality.
This situation is unacceptable,
Especially in science, the nominated interpreter
of reality!
Dumb idea 2
Wrong!
We need a New Enlightenment,
Where scientists directly control computation.
The only way to do this,
Is to teach scientists to program and let them do
it.
25
BioBike enables biocomputation for molecular
biologists.
BioBikes goals Give scientists direct control
over the discovery process. Provide access to
all the desired biological knowledge. Let the
scientists actually do the programming. Embed
biocomputing in a collaborative community of
biologists working together on problems.
BioBikes successes Knowledge OS does offer
unprecedented integration.
BioBikes failures The scientists didnt
actually do the programming!
BUT! A community did arise that did do the work!
26
KnowOS Integrated Knowledge Server
KnowOS
Biocomputational Tools and Sims
27
The Problem
Software Engineers are the Priests of the Modern
Age,
A mysterious cult standing between The People and
Reality.
This situation is unacceptable,
Especially in science, the nominated interpreter
of reality!
Probably dumb idea 3
We need a New Enlightenment,
Where scientists interact as peers with software
engineers.
One way to do this,
Is to make scientists interactional experts in
computing, and programmers interactional experts
in science, and put them together in communities.
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Applied Interactional Expertise in Scientific
Trading Zones
Verus?
T-Shaped People?
Communities of obsessive mad people engaged
through knowledge trading technologies