H LópezFernández M ReboiroJato D Glez Peña R Laza R Pavón F Fdez Riverola Bioinformatics Open Days 2018 Introduction Introduction Graphical User Interface ID: 807060
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Slide1
Lessons learned developing GUI in bioinformatics software: from end-user applications to resources for programmers
H.
López-Fernández
, M
.
Reboiro-Jato, D. Glez-Peña, R. Laza, R. Pavón, F. Fdez-RiverolaBioinformatics Open Days 2018
Slide2Introduction
Slide3Introduction
Graphical User Interface
Command Line Interface
Flexibility
Needed skills
Development time
Community demand
Slide4Introduction
Our
first
bioinformatics
GUI: geneCBR
Slide5Introduction
geneCBR
AIBench
http://www.aibench.org/
Slide6The AIBench framework
Slide7AIBench
Common requirements in scientific applications:Logging and process monitoringSetting a variable number of parametersChain user operations
Automatic GUI generationReuse previous operations (or plugins)
http://www.aibench.org
Slide8AIBench
CORE
PLUGINS ENGINEWORKBENCH
APPLICATION
CODE
Context-dependent
classes
/ third-party
libraries
Datatype 1
Datatype 3
Datatype 1
Operation
1
Operation
2
AIBench-
based
application
View 2
View 1
AIB
ench
CODE
JAVA VIRTUAL MACHINE
Developing with AIBench: operations, datatypes and views
http://
www.aibench.org
Slide9AIBench
Some applications developed with AIBench:Mass-Up (http://www.sing-group.org/mass-up/)LA-iMageS
(http://www.la-images.net/)OptFlux (http://www.optflux.org/)S2P (http://www.sing-group.org/s2p/)
@Note (http://
sysbio.di.uminho.pt/anote/wiki/index.php/Main_Page)
http://www.aibench.org
Slide10AIBench: Mass-Up
http://
www.aibench.org
Slide11AIBench
CORE
PLUGINS ENGINEWORKBENCH
APPLICATION
CODE
Context-dependent
classes
/ third-party
libraries
Datatype 1
Datatype 3
Datatype 1
Operation
1
Operation
2
AIBench-
based
application
View 2
View 1
AIB
ench
CODE
JAVA VIRTUAL MACHINE
Poor code reusing on
views
http://
www.aibench.org
Slide12AIBench
Poor code reusing on views
http://www.aibench.org
Slide13GC4S
Slide14GC4S
Aim: provide a library of high-level reusable GUI components
http://www.sing-group.org/gc4s
Slide15GC4S
Some applications developed with GC4S:With AIBench:S2P
(http://www.sing-group.org/s2p/)DEWE (http://www.sing-group.org/dewe)Without AIBench:SEDA (http://www.sing-group.org/seda
/)
http://
www.sing-group.org/gc4s
Slide16GC4S
SEDA (http://www.sing-group.org/seda/)
http://www.sing-group.org/gc4s
Check
out our poster!
Slide17Conclusions
Slide18Conclusions
Successfully developed bioinformatics GUIResources to increase programmers’ productivity: AIBench and GC4S
Open source, available at:https://github.com/sing-group
Slide19Acknowledgements
Centro Singular de Investigación de Galicia 2016-2019
Norte-01-0145-FEDER-000008
Porto
Neurosciences and Neurologic Disease Research Initiative at i3S
Slide20References
D. Glez-Peña; M. Reboiro-Jato; P. Maia; F. Díaz; F.
Fdez-Riverola (2010) AIBench: a rapid application development framework for translational research in biomedicine. Computer Methods and Programs in Biomedicine 98(2010), pp. 191-203. ISSN: 0169-2607. DOI: 10.1016/j.cmpb.2009.12.003
F.
Fdez-Riverola; D. Glez
-Peña; H. López-Fernández; M. Reboiro-Jato; J.R. Méndez (2012) A Java application framework for scientific software development. Software: Practice & Experience. Volume 42/8, pp. 1015-1036. ISSN: 0038-0644. DOI: 10.1002/spe.1108H. López-Fernández; M. Reboiro-Jato; D. Glez-Peña; J.R. Méndez-Reboredo; H.M. Santos; R.J. Carreira; J.L. Capelo; F. Fdez-Riverola (2011) Rapid development of proteomic applications with the AIBench framework
. Journal of
Integrative Bioinformatics
. 8/3:171. ISSN:
1613-4516. DOI:
10.2390/biecoll-jib-2011-171
H
. López-Fernández; M. Reboiro-Jato; J.A. Pérez-Rodríguez; F.
Fdez
-Riverola; D.
Glez
-Peña (2016)
The Artificial Intelligence Workbench: a retrospective review
. Advances in Distributed Computing and Artificial Intelligence Journal. Volume 5/1, pp. 73-85. ISSN: 2255-2863. DOI: 10.14201/ADCAIJ2016517385
Slide21Questions?
Bioinformatics Open Days
2018
Thank you!
Slide22This work is licensed under a Creative Commons Attribution-
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4.0 International License.