science gateways for life sciences – balancing usability and re-usability

Science Gateways for Life Sciences – Balancing Usability and Re-‐Usability

Sandra Gesing Center for Research Compu?ng

[email protected] 19 September 2013

Sandra Gesing

Life Sciences

2 Science Gateways for Life Sciences

“the sciences concerned with the study of living organisms, including biology, botany, zoology, microbiology, physiology, biochemistry, and related subjects” hMp://www.thefreedic?onary.com

•  Technologies and methods for crea?ng, analyzing and predic?on of data available

•  Immense amount of data, e.g., •  ZINC database: ~20 Mio molecular structures •  Human genome: ~ 3 Bio DNA base pairs

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Life Sciences and Computa?on


February 16, 2001 biotech company Celera

The Genomics Boom

February 15, 2001 The Human Genome Project

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Life Sciences and Computa?on


The Genomics Boom

Craig Venter (le`) and Francis Collins (right)

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Areas in the Life Sciences


•  A lot of “omics” sciences, e.g. •  Genomics •  Proteomics

Black Swallowtail -‐ larvae and buMerfly

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Molecular Simula?ons and Docking


•  Predic?on and analysis of molecular structures •  Numerous applica?ons, e.g. •  Materials science •  Drug design

ligands target

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Molecular Simula?ons and Docking


ligands target

docking binding energy scoring func?ons binding

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•  Predic?on and analysis of molecular structure •  Numerous applica?ons, e.g. •  Materials science •  Drug design

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Simula?ons


•  Basic data with heterogeneous provenance, e.g. Research in Malaria •  Data on weather •  Data on demography •  Data on interven?ons •  ...

•  Mathema?cal models needing a baseline •  Predic?on of interven?ons

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State-‐of-‐the-‐art


•  Data intensive and compute intensive problems •  Sophis?cated tools and methods available •  Distributed data management available •  DCIs (Distributed Compu?ng Infrastructures) available

Why do researchers not use the tools and distributed

environments on a large scale?

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Open Issues


•  Usability of tools o`en limited •  Complexity of methods •  Lack of graphical user interfaces

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Open Issues


•  Usability of tools o`en limited •  Complexity of methods •  Lack of graphical user interfaces •  Workflows

a sequence of connected steps in a defined order based on their control and data dependencies

Sandra Gesing

Open Issues


•  Usability of tools o`en limited •  Complexity of methods •  Lack of graphical user interfaces •  Workflows

a sequence of connected steps in a defined order based on their control and data dependencies

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Slide copied from: Stuart Owen „Workflows with Taverna“

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Open Issues


•  Usability of tools o`en limited •  Complexity of methods •  Lack of graphical user interfaces •  Workflows •  Complexity of infrastructures •  Users are generally not IT specialists

Sandra Gesing

Open Issues


•  Usability of tools o`en limited •  Complexity of methods •  Lack of graphical user interfaces •  Workflows •  Complexity of infrastructures •  Users are generally not IT specialists ⇒ User interfaces need to be intui8ve and self-‐ explanatory

⇒ Science gateways

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Science Gateways


“A Science Gateway is a community-‐developed set of tools, applica9ons, and data that is integrated via a portal or a suite of applica9ons, usually in a graphical user interface, that is further customized to meet the needs of a specific community.” TeraGrid/XSEDE

Community

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Web-‐based Science Gateways


•  Single point of entry •  Possibility to customize views and tools •  Store user preferences •  No installa?on of so`ware on the user’s side •  No firewall issues

Slar9barGast: “I must warn you, we're going to pass through, well, a sort of gateway thing.” Arthur Dent: „What?“ Slar9barGast: “It may disturb you. It scares the willies out of me.” (Douglas Adams in “The Hitchhiker's Guide to the Galaxy”)

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Goal of Science Gateways


Usability of so`ware "AOer all, usability really just means that making sure that something works well: that a person … can use the thing -‐ whether it's a Web site, a fighter jet, or a revolving door -‐ for its intended purpose without geSng hopelessly frustrated." (Steve Krug in “Don't make me think!: A Common Sense Approach to Web Usability”, 2005)

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Re-‐Usability


• Sharing of knowledge and data • Re-‐Using of „recipes“ and workflows • Re-‐Usability of so`ware “The key to produc9vity is reusability. The easiest way to produce code is obviously to have it already!" (John R. Bourne in “Object-‐oriented Engineering: Building Engineering Systems Using Smalltalk-‐80”, 1992)

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Re-‐Usability


Re-‐inven?ng is not always necessary...

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Re-‐Usability


... but the model should fit to the demands of the community

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Diverse Approaches


•  Science gateway frameworks •  Sta?c layout •  Layout extendable •  Workflow-‐enabled

•  Portal frameworks •  Content management systems •  Libraries for implementa?on

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Galaxy


Python framework

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Galaxy


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Parametriza?on


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Workflows


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Administra?on


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WS-‐PGRADE


User Interface WS-‐PGRADE

Liferay

DCI Resources Middleware Layer

High-‐Level Middleware Service Layer

gUSE

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WS-‐PGRADE


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Job Configura?on


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Monitoring


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MoSGrid


Molecular Simula?on Grid •  Science gateway integrated with underlying compute and data management infrastructure •  Distributed workflow management •  Data repository

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Tools


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File Management


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MoSGrid – Applica?on Areas


Molecular Dynamics •  Study and simula?on of molecular mo?on Quantum Chemistry •  Study and simula?on of molecular electronic behavior rela?ve to their chemical reac?vity Docking •  Main focus on evalua?on of ligand-‐receptor interac?ons (e.g., for drug design)

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MD Portlet


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QC Portlet


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Docking Portlet


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VectorBase


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Tools


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VECNet


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Data


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Modeling Plarorm


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Risk Mapper


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Usability vs. Re-‐Usability


•  User side •  Methods •  Workflows •  Data è Re-‐usability increases usability on the user side

•  Admin/Developer side •  Frameworks •  Libraries •  Source code è Usability and re-‐usability depend on support,

documenta?on and scalability

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Usability vs. Re-‐Usability


•  User side •  Layout •  Visualiza?on •  Security è Re-‐used parts may be not sufficient, usability depends on the features needed in the community

•  Admin/Developer side •  Integra?on with compu?ng and data infrastructures •  Security è Usability and re-‐usability depend on available infrastructures

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New Science Gateway -‐ Checklist


•  Demands of the user community on the user interface •  Demands on security •  Demands on compu?ng and data resources •  Workflows •  Performance

•  Exis?ng tools and models •  Available underlying infrastructure •  Available documenta?on and support •  Effort on development and maintenance

Sandra Gesing 56 Science Gatewazs for Life Sciences

[email protected]

science gateways for life sciences – balancing usability and re-usability

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