Usability and Bioinformatics Experience and Challenges Davide Bolchini University College London, Dept. Computer Science University of Lugano, Faculty of Communication Sciences, TEC-Lab Joint work with Anthony Finkelstein (UCL), Vito Perrone (UCL), Paolo Paolini (POLIMI and USI), Luca Mainetti (UNILE) Seminar at City University, London, Centre for HCI Design – 2 May 2008

The context web and bioinformatics applications Research goal improve usability and disseminate design knowledge Ongoing work results and challenges Roadmap for future work Outline

The context

web and bioinformatics applications

Research goal

improve usability and disseminate design knowledge

Ongoing work

results and challenges

Roadmap for future work

The context

Bioinformatics (or computational biology): applying computer science tools to the analysis, management and integration of biological information - genes, genomes, proteins, cells, clinical information - * The aim is to elucidate biological processes Huge sets of biological data are made publicly accessibile via several databases and repositories Web applications are designed on top to disseminate, access, share, cross-reference and manipulate those data. * Adapted from Sylvia B. Nagl „Introduction to Bioinformatics“ – UCL introductory bioinformatics course 2008 Web applications in bioinformatics

Bioinformatics (or computational biology): applying computer science tools to the analysis, management and integration of biological information - genes, genomes, proteins, cells, clinical information - *

The aim is to elucidate biological processes

Huge sets of biological data are made publicly accessibile via several databases and repositories

Web applications are designed on top to disseminate, access, share, cross-reference and manipulate those data.

Bioinformatics researchers Biomedical, industrial researchers use, feed design, use, feed […] designers, developers „ biologists“, „wet“ scientists

Contents Proteins, protein structures, functions, sequences, genes, genomes, experimental data, clinical evidence, … Applications Hundreds of web repositories being developed, published and updated Evolution Originally designed by a local team, they become relevant to a wider audience, used for different purposes in different contexts by different people Design quality and usability for the end users (biologists) do not always accompany this process A world of etherogenous resources

Contents

Proteins, protein structures, functions, sequences, genes, genomes, experimental data, clinical evidence, …

Applications

Hundreds of web repositories being developed, published and updated

Evolution

Originally designed by a local team, they become relevant to a wider audience, used for different purposes in different contexts by different people

Design quality and usability for the end users (biologists) do not always accompany this process

Biologists : research/task support, accessibility, findability, usability Bioinformaticians : accuracy of data, availability Developers : efficient design/delivery/implementation, maintainability, … Financial partners/funding orgs : „effectiveness“ and „impact“ of the applications funded (usages, satisfaction, „improvement in work“): better science … Stakeholders‘ concerns

Biologists : research/task support, accessibility, findability, usability

Bioinformaticians : accuracy of data, availability

Developers : efficient design/delivery/implementation, maintainability, …

Financial partners/funding orgs : „effectiveness“ and „impact“ of the applications funded (usages, satisfaction, „improvement in work“): better science

…

Effort, emphasis and primary funding focussed on content production and dissemination of results Limited attention – so far – to ensure actual usability of the bioinformatics applications for the biologists Enhanced usability of the resources can Enable life science researchers to exploit the full potential of the data Generate wider adoption Decrease the cost of technical support Increase trust imputed to groups/institution Better support them in their work and gain further insights (better science) Motivation for the work

Effort, emphasis and primary funding focussed on content production and dissemination of results

Limited attention – so far – to ensure actual usability of the bioinformatics applications for the biologists

Enhanced usability of the resources can

Enable life science researchers to exploit the full potential of the data

Generate wider adoption

Decrease the cost of technical support

Increase trust imputed to groups/institution

Better support them in their work and gain further insights (better science)

Research Goals

Improve the usability of web bioinformatics resources „ making the design right“ Ensure the usability of existing applications „ making the right design“ Re-understand the requirements and provide an enhanced, advanced support for biologists‘ work Generate bottom-up awareness in the bioinf. community Provide (transfer) tools (methods, patterns, guidelines) to designers to develop applications meeting the requirements of all stakeholders Goals

Improve the usability of web bioinformatics resources

„ making the design right“

Ensure the usability of existing applications

„ making the right design“

Re-understand the requirements and provide an enhanced, advanced support for biologists‘ work

Generate bottom-up awareness in the bioinf. community

Provide (transfer) tools (methods, patterns, guidelines) to designers to develop applications meeting the requirements of all stakeholders

Effort in building integrated interfaces over repositories (Javaheri) Advanced visualization techniques ( Hochheiser, Shneiderman ) Analysis of information-driven activities (Bartlett) Classification of tasks (Stevens) Is this enough? What investigating design and usability issues? Related Research

Effort in building integrated interfaces over repositories (Javaheri)

Advanced visualization techniques ( Hochheiser, Shneiderman )

Analysis of information-driven activities (Bartlett)

Classification of tasks (Stevens)

Is this enough? What investigating design and usability issues?

Ongoing work & results

Characterizing usability problems in bioinformatics Usability analysis of a sample of well-known applications Usability inspection on a protein classification web application (CATH) [browsing] User testing on three major repositories (NCBI, SwissProt, BioCarta) [search] Crafting more usable design solutions Understanding usability

Characterizing usability problems in bioinformatics

Usability analysis of a sample of well-known applications

Usability inspection on a protein classification web application (CATH) [browsing]

User testing on three major repositories (NCBI, SwissProt, BioCarta) [search]

Crafting more usable design solutions

Concept 4.0 – April 08 Protein Classification: Advanced Browsing

Protein classification based on a hierarchical model Each hierarchy level groups proteins with similar characteristics (based on structure, sequence, functional properties) E.g. CATH, SCOP repositories Protein Classification

Protein classification based on a hierarchical model

Each hierarchy level groups proteins with similar characteristics (based on structure, sequence, functional properties)

E.g. CATH, SCOP repositories

Hierarchical classifications are typically turned into hierarchical navigation models Pure tree navigation structures with many levels (7-8) Prone to offer rigid navigation mechanisms Protein Classification

Hierarchical classifications are typically turned into hierarchical navigation models

Pure tree navigation structures

with many levels (7-8)

Prone to offer rigid navigation mechanisms

Current information architecture and navigation: CATH

Tree-based navigation At each level access is granted to nodes to the immediate next level nodes further down on the hierarchy are not directly accessible To reach leaf nodes (protein domains) the user is forced to traverse all the levels of the hierarchy There is a necessary access sequence the user is forced to follow Effective when the user is able to specify upfront the values of all (8) parameters of the hierarchy, in order to locate a protein domain Less effective when users have more ill-defined knowledge of the classification parameters, need exploring and iteratively refining the browsing scope Opportunities for improvement

Tree-based navigation

At each level

access is granted to nodes to the immediate next level

nodes further down on the hierarchy are not directly accessible

To reach leaf nodes (protein domains) the user is forced to traverse all the levels of the hierarchy

There is a necessary access sequence the user is forced to follow

Effective when the user is able to specify upfront the values of all (8) parameters of the hierarchy, in order to locate a protein domain

Less effective when users have more ill-defined knowledge of the classification parameters, need exploring and iteratively refining the browsing scope

The challenge is decoupling Information architecture Hierarchical Useful to represent the domain knowledge Metting specific needs of bioinformaticians? Navigation/interaction paradigms on top Many are possible (including hierarchical ones) Supporting a more open-ended set of potential access and exploration tasks Useful to browse effectively and efficiently, according to various user’s needs, especially those of biologists Challenge

The challenge is decoupling

Information architecture

Hierarchical

Useful to represent the domain knowledge

Metting specific needs of bioinformaticians?

Navigation/interaction paradigms on top

Many are possible (including hierarchical ones)

Supporting a more open-ended set of potential access and exploration tasks

Useful to browse effectively and efficiently, according to various user’s needs, especially those of biologists

Preliminary high-level concept

Each classification criterion (hierarchy level) is modelled as a primary navigation dimension (facet or trail) It can be „projected“ to any other sublevel to facilitate the representation and visualization of the information Hypermedia remodelling Basic Design Paradigm

Each classification criterion (hierarchy level) is modelled as a primary navigation dimension (facet or trail)

It can be „projected“ to any other sublevel to facilitate the representation and visualization of the information

Hypermedia remodelling

beta Navigating the Protein Classification Class Architecture Topology Homologous Superfamily + + + +

Remodel the entire hierarchy into a semi-flat structure Made of mini-hierarchies of facets-values, or groups of trails Basic Design Paradigm

Remodel the entire hierarchy into a semi-flat structure

Made of mini-hierarchies of facets-values, or groups of trails

beta Navigating the Protein Classification Class Architecture Topology Homologous Superfamily - - - - Mainly Alpha Mainly Beta Mixed Alpha-Beta Few Secondary Structures Orthogonal Bundle Up-down Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel Ribbon Single Sheet Roll Beta Barrel Sandwich Distorted Sandwich Trefoil Orthogonal Prism ... (4) (40) (1084) (2091) Single alpha-helices Heat-Stable Enterotoxin B F1FO ATP Synthase Pheromone ER-1 Methane Monooxygenase Chorismate Mutase Domain Acyl-CoA Binding Protein Receptor-associated Protein ADP Ribosyl Cyclase Phospholipase A2 Chitosanase ... Protein binding High density lipoproteins Coiled-coil Complex (site-specific ... Blood coagulation Blood coagulation Integral membrane protein Virus coat protein Regulatory protein Oxidoreductase Transport protein Proteasome activator ...

1. Visualizing the distribution between classification levels

Topology (1084) + beta Filter classification by: Navigating the Protein Classification (13) (3) How superfamilies are distributed among topologies? How superfamilies are distributed among architectures? Which homologous superfamilies have architecture „alpha horseshoe“? Which topologies have architecture „alpha horseshoe“? . . . What are the class „alpha“ topologies? What are the class „alpha“ architectures? How many protein domains are there in each class? ... Architecture (40) + Class (4) + Homologous Superfamily (2091) + Ribbon [… domains] Single Sheet Roll Beta Barrel [… domains] Clam [… domains] Sandwich Distorted Sandwich [… domains] Trefoil Orthogonal Bundle [… domains] Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel Updown Bundle Sort by: name | domains | code Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ] Class 1: Mainly Alpha [ 19729 domains ] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain]

How superfamilies are distributed among topologies?

How superfamilies are distributed among architectures?

Which homologous superfamilies have architecture „alpha horseshoe“?

Which topologies have architecture „alpha horseshoe“?

. . .

What are the class „alpha“ topologies?

What are the class „alpha“ architectures?

How many protein domains are there in each class?

...

Gaining insights about the cardinality of the protein classes, and their relationships Skipping levels of the hierarchy (top-down) to visualize relative distribution Applicable to further sequence levels (SOLID) from any major level (CATH) Potential Benefits

Gaining insights about the cardinality of the protein classes, and their relationships

Skipping levels of the hierarchy (top-down) to visualize relative distribution

Applicable to further sequence levels (SOLID) from any major level (CATH)

2. Navigating the full protein collection by any criterion

beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 16 out of 443 domains Class (4) Topology (1084) Homologous Superfamily (2091) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + + + Sort by: name | domains | code 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 Architecture (40) _ 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02

Faceted navigation Any classification dimension can be independently used as suitable criterion for accessing the protein domains Browsing ALL the protein domain instances for any dimension (facet, hypertext trail) No need to traverse all the levels to reach the protein domains Potential Benefits

Faceted navigation

Any classification dimension can be independently used as suitable criterion for accessing the protein domains

Browsing ALL the protein domain instances for any dimension (facet, hypertext trail)

No need to traverse all the levels to reach the protein domains

3. Superimposing multiple classifications while browsing the protein collection

beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 16 out of 443 domains Class (4) Topology (3) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + - Sort by: name | domains | code Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ]

beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 16 out of 443 domains Class (4) Topology (3) Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] + - Sort by: name | domains | code (13) T, H T T Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ] Homologous Superfamily (2091) + Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain]

...with progressive filtering

beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A05 4mu4A01 1mu5A02 3 out of 59 domains Class (4) Topology (3) Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] + - Sort by: name | domains | code (13) T, H T T Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ] Homologous Superfamily (2091) + Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain] 70-kda Soluble Lytic Transglycosylase, domain 1 [3 domains] Leucine-rich Repeat Variant [89 domains] Lipovitellin. Chain A, domain 2 [1 domain] IP3 receptor type 1 binding core, domain 2 [1 domain]

4. Associative navigation from the protein details

beta Filter classification by: Navigating the Protein Classification Class (4) Topology (3) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + - Sort by: name | domains | code Protein Domain: 1eyhA00 ATOM Sequence HNYSEAEIKVREATSNDPWGPSSSLMSEIADLTYNVVAFSEIMSMIWKRLNDHGKNWRHVYKAMTLMEYLIKTGSERVSQ QCKENMYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDRLREERAHALKTKEKLAQTA COMBS Sequence HNYSEAEIKVREATSNDPWGPSSSLMSEIADLTYNVVAFSEIMSMIWKRLNDHGKNWRHVYKAMTLMEYLIKTGSERVSQ QCKENMYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDRLREERAHALKTKEKLAQTA >> Chain: 1eyhA Summary Chain ID 1eyhA Insert Timestamp 05 Mar 2006 13:03 PDB code 1eyh Flow Stage Type Chopped Seq Length 144 Fraction of Non-Alpha Carbon Atoms 0.88 Chain History Chain chopped (05 Mar 2006: Auto) PDB chopped based on information from the domall file >> Pdb: 1eyh Status PDB code 1eyh Release Date 06 May 2000 Release Status PDB_RELEASE_STATUS_ACTIVE Superseded Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ] See also domains of the same:  Class: alpha (19‘729 domains)  Architecture: alpha horseshoe (443 domains)  Topology: Serine… (349 domains)  Homologous Superfamily: cell cycle (46 domains) [by other levels]

beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 16 out of 443 domains Class (4) Topology (1084) Homologous Superfamily (2091) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + + + Sort by: name | domains | code Architecture (40) _

Enhance serendipity in the user experience Discover new proteins sharing properties with a known one Encourage further exploration Potential Benefits

Enhance serendipity in the user experience

Discover new proteins sharing properties with a known one

Encourage further exploration

Push communication (notifying local updates)

beta Filter classification by: Navigating the Protein Classification Class (4) Topology (3) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + - Sort by: name | domains | code Protein Domain: 1eyhA00 ATOM Sequence HNYSEAEIKVREATSNDPWGPSSSLMSEIADLTYNVVAFSEIMSMIWKRLNDHGKNWRHVYKAMTLMEYLIKTGSERVSQ QCKENMYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDRLREERAHALKTKEKLAQTA COMBS Sequence HNYSEAEIKVREATSNDPWGPSSSLMSEIADLTYNVVAFSEIMSMIWKRLNDHGKNWRHVYKAMTLMEYLIKTGSERVSQ QCKENMYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDRLREERAHALKTKEKLAQTA >> Chain: 1eyhA Summary Chain ID 1eyhA Insert Timestamp 05 Mar 2006 13:03 PDB code 1eyh Flow Stage Type Chopped Seq Length 144 Fraction of Non-Alpha Carbon Atoms 0.88 Chain History Chain chopped (05 Mar 2006: Auto) PDB chopped based on information from the domall file >> Pdb: 1eyh Status PDB code 1eyh Release Date 06 May 2000 Release Status PDB_RELEASE_STATUS_ACTIVE Superseded XML populated as updates occur RSS Architecture (40) _ Leucine-rich Repeat Variant [ 91 domains ] 70-kda Soluble Lytic Transglycosylase; domain 1 [ 3 domains ] Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat [ 349 domains ] See also domains of the same:  Class: alpha (19‘729 domains)  Architecture: alpha horseshoe (443 domains)  Topology: Serine… (349 domains)  Homologous Superfamily: cell cycle (46 domains) […]

beta Filter classification by: Navigating the Protein Classification Protein Domains Architecture: Alpha Horseshoe (443 domains) 1mu5A02 1mu5A03 1mu5A05 4mu4A01 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 1mu5A02 16 out of 443 domains Class (4) Topology (1084) Homologous Superfamily (2091) Ribbon Single Sheet Roll Beta Barrel Clam Sandwich Distorted Sandwich Trefoil Orthogonal Bundle Updown Bundle Alpha Horseshoe [ 443 domains ] Alpha solenoid [6 domains] Alpha/alpha barrel [… domains] Beta Barrel Clam Distorted Sandwich Orthogonal Bundle Alpha Horseshoe Alpha solenoid Alpha/alpha barrel + + + Sort by: name | domains | code RSS XML populated as updates occur Architecture (40) _

For biologists Focussing long-term research on specific (limited number of) protein domain instances Follow updates and research evolution “ localized” proactive notification is important For bioinformaticians Working on large collections of data for computation purposes To be combined with data download facilities Input and ideas to the redesign of CATH Potential Benefits

For biologists

Focussing long-term research on specific (limited number of) protein domain instances

Follow updates and research evolution

“ localized” proactive notification is important

For bioinformaticians

Working on large collections of data for computation purposes

To be combined with data download facilities

Input and ideas to the redesign of CATH

Strategies to exploit the full potential of the information architecture based on protein classification Enhance usability and flexibility in accessing the protein collection Faceted navigation besides purely hierarchical access Hypertextual paths Setting more favorable conditions for serendipity and insights discovery Summary

Strategies to exploit the full potential of the information architecture based on protein classification

Enhance usability and flexibility in accessing the protein collection

Faceted navigation

besides purely hierarchical access

Hypertextual paths

Setting more favorable conditions for serendipity and insights discovery

Ongoing review, walkthrough of the design concept with bioinformaticians, and the CATH team at UCL Provoking reflection and reaction to design opportunities to gain insight into domain knowledge and requirements („the importance of ignorance“) Eliciting domain knowledge

Ongoing review, walkthrough of the design concept with bioinformaticians, and the CATH team at UCL

Provoking reflection and reaction to design opportunities to gain insight into domain knowledge and requirements

(„the importance of ignorance“)

Capture user requirements of: Biologists Bioinformaticians In terms of: Goals in using the current classification Access and data manipulation tasks Start from recruiting current CATH users Refine, validate the design concept Implement a generic system architecture and make it available Next steps

Capture user requirements of:

Biologists

Bioinformaticians

In terms of:

Goals in using the current classification

Access and data manipulation tasks

Start from recruiting current CATH users

Refine, validate the design concept

Implement a generic system architecture and make it available

Davide Bolchini [email_address] http://bolchini.blogspot.com http://www.cs.ucl.ac.uk/staff/D.Bolchini/ Contacts

Davide Bolchini

[email_address]

http://bolchini.blogspot.com

http://www.cs.ucl.ac.uk/staff/D.Bolchini/