Programming or Flexibility? Design of Programmable Applications with - - PowerPoint PPT Presentation

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Programming or Flexibility? Design of Programmable Applications with - - PowerPoint PPT Presentation

Feb 11, 2024 124 likes •659 views

Programming or Flexibility? Design of Programmable Applications with Biologists Catherine Letondal letondal@pasteur.fr In Situ, LRI, Institut Pasteur EUD-Net p.1/22 In Situ New interaction paradigms: multi-scale (or zoomable)

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Programming or Flexibility?

Design of Programmable Applications with Biologists

Catherine Letondal

letondal@pasteur.fr

In Situ, LRI, Institut Pasteur

EUD-Net – p.1/22

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In Situ

New interaction paradigms: multi-scale (or zoomable) interfaces, interactive information visualization, bimanual interaction, video and non-speech audio, augmented or mixed reality. Participatory design development of new participatory design methods, make the role of context explicit in the design process. Engineering of interactive systems component-based architectures (customizable and dynamic addition or substitution of interaction techniques).

EUD-Net – p.2/22

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Programming situations

scripting: search for a sequence pattern, then retrieve all the corresponding secondary structures in a database (example)

EUD-Net – p.3/22

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Programming situations

scripting: search for a sequence pattern, then retrieve all the corresponding secondary structures in a database (example) parsing: search for the best match in a database similarity search report but relative to each subsection

EUD-Net – p.3/22

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Programming situations

scripting: search for a sequence pattern, then retrieve all the corresponding secondary structures in a database (example) parsing: search for the best match in a database similarity search report but relative to each subsection formatting: renumber one’s sequence positions from

  • 3000 to +500 instead of 0 to 3500

EUD-Net – p.3/22

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Programming situations

scripting: search for a sequence pattern, then retrieve all the corresponding secondary structures in a database (example) parsing: search for the best match in a database similarity search report but relative to each subsection formatting: renumber one’s sequence positions from

  • 3000 to +500 instead of 0 to 3500

variation: search for patterns in a sequence, except repeated ones

EUD-Net – p.3/22

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Programming situations

scripting: search for a sequence pattern, then retrieve all the corresponding secondary structures in a database (example) parsing: search for the best match in a database similarity search report but relative to each subsection formatting: renumber one’s sequence positions from

  • 3000 to +500 instead of 0 to 3500

variation: search for patterns in a sequence, except repeated ones finer control on the computation: control in what order multiple sequences are compared and aligned

EUD-Net – p.3/22

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Programming situations

scripting: search for a sequence pattern, then retrieve all the corresponding secondary structures in a database (example) parsing: search for the best match in a database similarity search report but relative to each subsection formatting: renumber one’s sequence positions from

  • 3000 to +500 instead of 0 to 3500

variation: search for patterns in a sequence, except repeated ones finer control on the computation: control in what order multiple sequences are compared and aligned simple operations: search in a DNA sequence for the characters other than A, C, T and G

EUD-Net – p.3/22

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Parsing and scripting example

This example shows the report of a program searching for registered well-known patterns in a given protein sequence. Access# From->To Name _______ ________ ____ PS00005 39->41 PKC_PHOSPHO_SITE Pattern [ST].[RK] matched Site 39 TTR 41 PS00005 71->73 PKC_PHOSPHO_SITE Pattern [ST].[RK] matched Site 71 TSK 73 PS00008 20->25 MYRISTYL Pattern G[ˆEDRKHPFYW]..[STAGCN][ˆP] matched Site 20 GILAAI 25

EUD-Net – p.4/22

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Problem description

more and more professional bio-informaticists, still a minority the vast majority does not program

EUD-Net – p.5/22

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Problem description

more and more professional bio-informaticists, still a minority the vast majority does not program many biologists are able to program and have learned programming many of them do not program at all although they would need it

EUD-Net – p.5/22

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Problem description

more and more professional bio-informaticists, still a minority the vast majority does not program many biologists are able to program and have learned programming many of them do not program at all although they would need it

Why?

EUD-Net – p.5/22

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Problem description

more and more professional bio-informaticists, still a minority the vast majority does not program many biologists are able to program and have learned programming many of them do not program at all although they would need it It’s too difficult to program a little.

EUD-Net – p.5/22

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Approaches

enable Programming In The User Interface (programmability)

EUD-Net – p.6/22

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Programming In The User Interface

What we want:

= programming environment working environment

EUD-Net – p.7/22

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biok: graphical objects

EUD-Net – p.8/22

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biok: tags

EUD-Net – p.9/22

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biok: programming tags

EUD-Net – p.10/22

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biok: tags classes

RegexpRowTag Tag SequenceTag RowTag ColTag CellRowTag CellColTag GCTag PIDTag OccTag PatternTag ToppredTag CellTag PyrPurTag ZappoTag

EUD-Net – p.11/22

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biok: sub-classing tags

EUD-Net – p.12/22

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biok: sub-classing tags

EUD-Net – p.12/22

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biok: programming

EUD-Net – p.13/22

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biok programming: tracing

EUD-Net – p.14/22

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Programming In The User Interface

= programming environment working environment

learning by examples incremental programming easier switch between 2 modes (using/programming); programming as just a kind of advanced use (with several levels) (but programming should not be required for a standard use)

EUD-Net – p.15/22

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Approaches

enable Programming In The User Interface (programmability)

EUD-Net – p.16/22

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Approaches

enable Programming In The User Interface (programmability) from programmability to software flexibity; for biologists, lack of flexibility in current software could provide a better explanation than technical or cognitive problems in programming

EUD-Net – p.16/22

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Approaches

enable Programming In The User Interface (programmability) from programmability to software flexibity; for biologists, lack of flexibility in current software could provide a better explanation than technical or cognitive problems in programming flexibility is anticipation:

EUD-Net – p.16/22

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Approaches

enable Programming In The User Interface (programmability) from programmability to software flexibity; for biologists, lack of flexibility in current software could provide a better explanation than technical or cognitive problems in programming flexibility is anticipation: programmability

EUD-Net – p.16/22

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Approaches

enable Programming In The User Interface (programmability) from programmability to software flexibity; for biologists, lack of flexibility in current software could provide a better explanation than technical or cognitive problems in programming flexibility is anticipation: programmability MOP

EUD-Net – p.16/22

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Modifiable systems

Cognitive distance issue:

user interface program objects UI objects source code domain objects user

EUD-Net – p.17/22

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Modifiable systems

Cognitive distance issue:

source code user user interface A good programming environment

EUD-Net – p.17/22

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Modifiable systems

Cognitive distance issue:

source code user user interface A good programming environment

From MOP ...

user language define modify meta−model (MOP, ...) programs with

EUD-Net – p.17/22

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Modifiable systems

Cognitive distance issue:

source code user user interface A good programming environment

From MOP ... to MAP (Meta-Application Protocol):

user language define modify meta−model (MOP, ...) programs with user application uses define modify meta−model (internal representation)

EUD-Net – p.17/22

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Modifiable systems

Cognitive distance issue:

source code user user interface

intermediate progr. levels (protocol)

A good programming environment

From MOP ... to MAP (Meta-Application Protocol):

user language define modify meta−model (MOP, ...) programs with user application uses define modify meta−model (internal representation)

EUD-Net – p.17/22

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Approaches

enable Programming In The User Interface (programmability) from programmability to software flexibity; for biologists, lack of flexibility in current software could provide a better explanation than technical or cognitive problems in programming flexibility is anticipation: programmability MOP participatory design,

EUD-Net – p.18/22

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Participatory Design

anticipate flexibility spots (EU-not-P versus EUP)

programming use direct

EUD-Net – p.19/22

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Participatory Design

rather few programming issues raised in design workshops

EUD-Net – p.19/22

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Approaches

enable Programming In The User Interface (programmability) from programmability to software flexibity; for biologists, lack of flexibility in current software could provide a better explanation than technical or cognitive problems in programming flexibility is anticipation: programmability MOP participatory design, flexibility is provided in informal tools (spreadsheets, ...), flexibility is also more control on computation, (algorithmic flexibility)

EUD-Net – p.20/22

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Algorithmic flexibility

A way to integrate user’s knowledge in computation neither as parameter nor as programming (using interception techniques (AOP?)).

differences in results are highlighted

< 20 certain certain certain certain user certainmod user defined segment (supersedes next peak) peak is too close segment could be predicted with user indication without user indication

EUD-Net – p.21/22

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Conclusions

Context:

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ...

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal Approach:

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal Approach: user-development also as a software design issue

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal Approach: user-development also as a software design issue participative programming

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal Approach: user-development also as a software design issue participative programming Who is Mr/Ms End-User...?

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal Approach: user-development also as a software design issue participative programming Who is Mr/Ms End-User...? the user of the software, e.g:

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal Approach: user-development also as a software design issue participative programming Who is Mr/Ms End-User...? the user of the software, e.g: the biologist,

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal Approach: user-development also as a software design issue participative programming Who is Mr/Ms End-User...? the user of the software, e.g: the biologist, ... (have you ever really tried to re-program emacs?)

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal Approach: user-development also as a software design issue participative programming Who is Mr/Ms End-User...? the user of the software, e.g: the biologist, ... (have you ever really tried to re-program emacs?) not defined by a skill level, rather by his/her role towards the software

EUD-Net – p.22/22

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Conclusions

Context: user studies: critical need for flexibility writing text code is ok for biologists ... ... although programming is not the goal Approach: user-development also as a software design issue participative programming Who is Mr/Ms End-User...? the user of the software, e.g: the biologist, ... (have you ever really tried to re-program emacs?) not defined by a skill level, rather by his/her role towards the software

EUD-Net – p.22/22