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Chemical Informatics tools, services and workflows. David Wild [email protected] http://www.informatics.indiana.edu/djwild. Outline. Chemical Informatics software packages available at IU Open source software The need for integration & innovation Pipelines, workflows and web services.

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david wild djwild@indiana edu http www informatics indiana edu djwild
Chemical Informatics tools, services and workflows

David Wild

[email protected]

http://www.informatics.indiana.edu/djwild

David Wild – I533 2006. Page 1

outline
Outline
  • Chemical Informatics software packages available at IU
  • Open source software
  • The need for integration & innovation
  • Pipelines, workflows and web services

David Wild – I533 2006. Page 2

software at iub informatics
Software at IUB Informatics
  • Spotfire DecisionSite
  • ChemTK
  • ArgusLab
  • BCI software – cluster analysis, fingerprints, Markush
  • OpenEye software – 3D conformer, docking
  • Chemaxon
  • gNova CHORD
  • Chemoinformatics programming toolkits
    • Daylight, BCI, OpenEye

David Wild – I533 2006. Page 3

open source free software
Open Source / Free Software
  • Blue Obelisk - http://wiki.cubic.uni-koeln.de/dokuwiki/doku.php
  • InChI - http://www.iupac.org/inchi/
  • JMOL – http://jmol.sourceforge.net
  • FROWNS - http://frowns.sourceforge.net/
  • OpenBabel - http://openbabel.sourceforge.net/
  • CML - http://cml.sourceforge.net/
  • CDK - http://almost.cubic.uni-koeln.de/cdk/
  • MMTK - http://starship.python.net/crew/hinsen/MMTK/

David Wild – I533 2006. Page 4

the need for integration
The need for integration
  • Research computing is currently very fragmented
  • Existing approaches do not scale up to the amount of data now common
  • Many chemical informatics tools are obscure, difficult to use and access
  • Scientists’ questions are not that complex, but finding the answers is currently very time consuming and/or complex (for a human)
    • “has anybody patented this chemical structure I just made?”
    • “can I get hold of a compound that might bind to the active site of this protein I just resolved?”
    • “which compounds in this series are least likely to exhibit toxic effects?”
  • Answers are often “stale” after a short period of time – questions need to be re-answered as new information is generated
  • Almost all available systems are passive, and follow the(web) browsing model
  • There tends to be one interface for every data source(or encompassing just a few)

David Wild – I533 2006. Page 5

slide6
Word Document (Marketing)

Oracle Database (HTS)

Journal Article

Oracle Database (Genomics)

Computation

Word Document (Chemistry)

External Database (Patent)

Computation

Excel Spreadsheet (Toxicity)

 All the compounds pass the Lipinksi Rule of Five and toxicity filters

 A report by a team in Marketing casts doubt on whether the market for this target is big enough to make development cost-effective

Compounds were tested against related assays and showed activity, including selectivity within target families

? None of these compounds have been tested in a microarray assay

 One of the compounds was previously tested for toxicology and was found to have no liver toxicity

 A recent journal article reported the effectiveness of some compounds in a related series against a target in the same family

 Some structures with a similarity > 0.75 to these appear to be covered by a patent held by a competitor

 Several of the compounds had been followed up in a previous project, and solubility problems prevented further development

 The information in the structures and known activity data is good enough to create a QSAR model with a confidence of 75%

?

SCIENTIST

“These compounds look promising from their HTS results. Should I commit some chemistry resources to following them up?”

David Wild – I533 2006. Page 6

pipelining and workflow tools
Pipelining and workflow tools
  • These tools permit applications to be “piped” together or connected in “workflows” where the output of one program can be given as input to another program (or script)
  • Graphical front ends are replacing scripting – e.g. PERL, Python, etc
  • Available graphical tools
    • Scitegic Pipeline Pilot - http://www.scitegic.com
    • Inforsense KDE - http://www.inforsense.com/
    • Taverna – http://taverna.sourceforge.net
    • IO-Informatics Sentient – http://www.io-informatics.com
  • Find their real power in a web services environment

David Wild – I533 2006. Page 7

web services
Web Services
  • Semantic Web – “Next Big Thing”
    • Encode semantics in web pages (XML)
    • Describes services as well as information (SOAP, WSDL, UDDI)
    • Computation detached from interface
    • Note seeping through to general web usage
      • http://www.google.com/apis/
      • http://www.amazon.com/webservices
  • eScience (UK)
    • £200m over 2001-2006 period
    • http://www.rcuk.ac.uk/escience/
  • Cyber Infrastructure / Grid (US)
    • Semantic Web Health Care & Life Sciences Research Group - http://www.w3.org/2001/sw/hcls/

David Wild – I533 2006. Page 11

cicc related projects
CICC-related projects
  • Formal CICC projects
    • Innovative cross-screen analysis of NIH DTP Human Tumor Cell Line Data – innovative scientific analysis of NIH HTS data
    • Development of cheminformatics web services and use cases in Taverna – web service & workflow infrastructure
    • Development of a novel interface for the analysis of PubChem HTS data – tools for interacting with lots of complex data
    • A structure storage and searching system for Distributed Drug Discovery – innovative kinds of chemical databases
  • Other, related projects
    • Fast clustering of very large datasets using Linux clusters
    • Smart client for mining drug discovery data (Microsoft supported)

David Wild – I533 2006. Page 12

slide13
SMART CLIENT

General drug discovery

web services

& workflows

SMART CLIENT

Smart interfaces (incl.

NLP, RSS, agents, etc)

SMART CLIENT

Smart interfaces (incl.

NLP, RSS, agents, etc)

PROJECT 2

Web services

& workflows

PROJECT 1

Innovative cross-screen

analysis of

HTS data

PROJECT 4

Experimental

Databases

PROJECT 3

Visualization, navigation

& analysis tools for

HTS data

FAST PARALLEL

CLUSTERING

Using DivKmeans

& AVIDD

David Wild – I533 2006. Page 13

desired outcomes by summer 2006
Desired outcomes by Summer 2006
  • A chemical informatics web service infrastructure running at IU
  • Several Taverna workflows that use these and other web services, and which demonstrate that the infrastructure can be used to perform complex, relevant operations on PubChem data
  • Demonstrated scientific results with the NIH DTP data
  • An established Distributed Drug Discovery database linked with PubChem, that shows that our techniques together with PubChem can be employed in ways which benefit humanity in general
  • A sandbox PubChem copy with improved functionality and architecture
  • One or more novel visualization tools for PubChem data
  • Demonstrate the feasibility of fast, accurate clustering of very large datasets (including the whole of PubChem) using the AVIDD Linux Cluster and a parallelized clustering algorithm (DivKmeans)
  • Show that .NET and Java-based web services can work well together in a common infrastructure
  • Demonstrate the feasibility of a natural language or other straightforward interface for scientists to express their information needs

David Wild – I533 2006. Page 14

slide15
SMILES + ID + Data

Fingerprint

Generator

BCI Makebits

Cluster

Analysis

BCI Divkmeans

NIH Database

Service

PostgreSQL

CHORD

SMILES + ID

Cluster

Membership

Table

Management

VoTables

Fingerprints

Cluster the compounds in the NIH DTP database by chemical structure, then choose representative compounds from the clusters and dock them into PDB protein files of interest

SMILES + ID + + Cluster # + Data

Plot

Visualizer

VoPlot

Docking

Selector

Script

3D Visualizer

JMOL

SMILES + ID

Docking

OpenEye FRED

2D-3D

OpenEye OMEGA

PDB Database

Service

Docked Complex

MOL File

PDB Structure + Box

David Wild – I533 2006. Page 15

slide16
“However large an array of facts, however rapidly they accumulate,

it is possible to keep them in order and to extract from

time to time digests containing the most generally significant

information, while indicating how to find those items of

specialized interest. To do so, however, requires the will

and the means”

“[we need to] get the best information in the minimum quantity

in the shortest time, from the people who are producing the

information to the people who want it, whether they know they

want it or not”

J.D. Bernal, quoted in Murray-Rust et. al., Org. Biomol. Chem., 2004, 2, 3192-3203

David Wild – I533 2006. Page 16

smart client for drug discovery
“Smart Client” for drug discovery

An open-source prototype that implements a new model of data mining that would, on request, “push” relevant information to pharmaceutical scientists in response to previously-defined straightforward expressions of needs, rather than relying on them stumbling upon the right information using traditional “browsing” models.

… using workflows and web services

David Wild – I533 2006. Page 17

slide20
Request from Human Interface

USE-CASE SCRIPT

Invoke New Structure Service

Convert structures to 3D

Dock results & protein file

Extract any hits

Return links for visualization

AGENT / SMART CLIENT

Parse request

Select appropriate use cases

and/or web service(s)

Schedule as necessary

UDDI

WSDL

SOAP

New Structure Service

Search online databases

for recent structures

Search local databases

for recent structures

Merge Results

Online

database

(e.g. PubChem)

Local

database

3D Docking

Tool

2D-3D

converter

3D

visualizer

atomic services

aggregate services

David Wild – I533 2006. Page 20

prototype development plan
Prototype development plan
  • Develop a handful of use-cases based around industry/academia scientists
  • Build 5-6 data / computation sources (e.g. enumeration, property calculation, structure database) that can fulfill the use cases
  • Build WSDL and SOAP web services around the data sources that can be accessed from Taverna
  • Develop workflows in Taverna (see taverna.sourceforge.net)
  • Publish web services in UDDI
  • Encode use-cases into scripts
  • Build Intelligent Agent / Smart Client node that can match user needs with scripts & web services using workflows
  • Develop browser interface through Contextual Inquiry/Usability Studies
  • Consider mapping to a Natural Language Interface

David Wild – I533 2006. Page 21

use case 1 are there any good ligands for my target
Use Case #1Are there any good ligands for my target?
  • A chemist is working on a project involving a particular protein target, and wants to know:
    • Any newly published compounds which might fit the protein receptor site
    • Any published 3D structures of the protein or of protein-ligand complexes
    • Any interactions of compounds with other proteins
    • Any information published on the protein target

David Wild – I533 2006. Page 22

use case 1 are there any good ligands for my target23
Use Case #1Are there any good ligands for my target?
  • A chemist is working on a project involving a particular protein target, and wants to know:
    • Any newly published compounds which might fit the protein receptor site  gNova / PostgreSQL, PubChem search, FRED Docking
    • Any published 3D structures of the protein or of protein-ligand complexes  PDB search
    • Any interactions of compounds with other proteins  gNova / PostgreSQL, PubChem search
    • Any information published on the protein target  Journal text search

David Wild – I533 2006. Page 23

use case 2 who else is working on these structures
Use Case #2Who else is working on these structures?
  • A chemist is working on a chemical series for a particular project and wants to know:
    • If anyone publishes anything using the same or related compounds
    • Any new compounds added to the corporate collection which are similar or related
    • If any patents are submitted that might overlap the compounds he is working on
    • Any pharmacological or toxicological results for those or related compounds
    • The results for any other projects for which those compounds were screened

David Wild – I533 2006. Page 24

use case 2 who else is working on these structures25
Use Case #2Who else is working on these structures?
  • A chemist is working on a chemical series for a particular project and wants to know:
    • If anyone publishes anything using the same or related compounds ~ PubChem search
    • Any new compounds added to the corporate collection which are similar or related  gNova CHORD / PostgreSQL
    • If any patents are submitted that might overlap the compounds he is working on~ BCI Markush handling software
    • Any pharmacological or toxicological results for those or related compounds  gNova CHORD / PostgreSQL, MiToolkit
    • The results for any other projects for which those compounds were screened  gNova CHORD / PostgreSQL, PubChem search

David Wild – I533 2006. Page 25

priorities for web service development
Priorities for web service development
  • Search of PubChem
    • Wrap around HTTP or SOAP request
  • Search of local gNova / PostgreSQL database
    • Wrap around application
  • Molecular docking with OpenEye FRED
    • Wrap around application
  • Property calculation with Molinspiration MiTools
    • Wrap around application
  • PDB Search
    • Already implemented as EMBL web service
  • BCI Markush search
    • Wrap around application
  • Fast clustering of large datasets
    • Wrap around grid-based application
  • Visualizations of datasets
    • Client and service development – VisualiSAR, Spotfire

David Wild – I533 2006. Page 26

use case cicc which of these hits should i follow up
Use Case - CICCWhich of these hits should I follow up?
  • An MLI HTS experiment has produced 10,000 possible hits out of a screening set of 2m compounds. A chemist at another laboratory wants to know if there are any interesting active series she might want to pursue, based on:
    • Structure-activity relationships
    • Chemical and pharmacokinetic properties
    • Compound history
    • Patentability
    • Toxicity
    • Synthetic feasibility

David Wild – I533 2006. Page 27

use case eccr which of these hits should i follow up
Use Case – ECCRWhich of these hits should I follow up?
  • An HTS experiment has produced 10,000 possible hits out of a screening set of 2m compounds. A chemist on the project wants to know what the most promising series of compounds for follow-up are, based on:
    • Series selection  cluster analysis
    • Structure-activity relationships  modal fingerprints/stigmata
    • Chemical and pharmacokinetic propertiesmitools, chemaxon
    • Compound history gNova / PostgreSQL
    • Patentability  BCI Markush handling software
    • Toxicity
    • Synthetic feasibility
    • + requires visualization tools!

David Wild – I533 2006. Page 28

technology
Technology
  • Perl SOAP::Lite
    • Will be used for initial web service development
    • Doesn’t really implement WSDL & UDDI
  • Apache Axis & Tomcat
    • Deploy WSDL for web services
  • BPEL4WS – Business Process Execution Language
    • For aggregation of web services
    • http://www-128.ibm.com/developerworks/library/specification/ws-bpel/
  • Microsoft .NET & C#

David Wild – I533 2006. Page 29

current activities
Current activities
  • Core activities
    • Development of use-cases
    • Development of initial web services (Perl SOAP::Lite)
    • Use of Taverna to prototype use-case scripts
  • Basic research on future components
    • Organizing large amounts of chemical informationfor human consumption
      • Development of very fast parallel clustering techniques – to be exposed as web services
    • Selection of interface-level tools for basic interaction
      • Chemical structure drawing, display
      • Investigation of email, NLP, RSS, and browser interfaces
    • Interface-level tools for visualization, navigation and analysis
      • Cluster and dataset visualization, natural language interfaces)

David Wild – I533 2006. Page 30

cluster analysis and chemical informatics
Cluster Analysis and Chemical Informatics
  • Used for organizing datasets into chemical series, to build predictive models, or to select representative compounds
  • Organizational usage has not been as well studies as the other two, but see
    • Wild, D.J., Blankley, C.J. Comparison of 2D Fingerprint Types and Hierarchy Level Selection Methods for Structural Grouping using Wards Clustering, Journal of Chemical Information and Computer Sciences., 2000, 40, 155-162.
  • Essentially helping large datasets become manageable
  • Methods used:
    • Jarvis-Patrick and variants
      • O(N2), single partition
    • Ward’s method
      • Hierarchical, regarded as best, but at least O(N2)
    • K-means
      • < O(N2), requires set no of clusters, a little “messy”
    • Sphere-exclusion (Butina)
      • Fast, simple, similar to JP
    • Kohonen network
      • Clusters arranged in 2D grid, ideal for visualization

David Wild – I533 2006. Page 31

limitations of ward s method for large datasets 1m
Limitations of Ward’s method forlarge datasets (>1m)
  • Best algorithms have O(N2) time requirement (RNN)
  • Requires random access to fingerprints
    • hence substantial memory requirements (O(N))
  • Problem of selection of best partition
    • can select desired number of clusters
  • Easily hit 4GB memory addressing limit on 32 bit machines
    • Approximately 2m compounds

David Wild – I533 2006. Page 32

scaling up clustering methods
Scaling up clustering methods
  • Parallelisation
    • Clustering algorithms can be adapted for multiple processors
    • Some algorithms more appropriate than others for particular architectures
    • Ward’s has been parallelized for shared memory machines, but overhead considerable
  • New methods and algorithms
    • Divisive (“bisecting”) K-means method
    • Hierarchical Divisive
    • Approx. O(NlogN)

David Wild – I533 2006. Page 33

divisive k means clustering
Divisive K-means Clustering
  • New hierarchical divisive method
    • Hierarchy built from top down, instead of bottom up
    • Divide complete dataset into two clusters
    • Continue dividing until all items are singletons
    • Each binary division done using K-means method
    • Originally proposed for document clustering
  • “Bisecting K-means”
    • Steinbach, Karypis and Kumar (Univ. Minnesota)http://www-users.cs.umn.edu/~karypis/publications/Papers/PDF/doccluster.pdf
    • Found to be more effective than agglomerative methods
    • Forms more uniformly-sized clusters at given level

David Wild – I533 2006. Page 34

bci divkmeans
BCI Divkmeans
  • Several options for detailed operation
    • Selection of next cluster for division
    • size, variance, diameter
    • affects selection of partitions from hierarchy, not shape of hierarchy
  • Options within each K-means division step
    • distance measure
    • choice of seeds
    • batch-mode or continuous update of centroids
    • termination criterion
  • Have developed parallel version for Linux clusters / grids in conjunction with BCI
  • For more information, see Barnard and Engels talks at: http://cisrg.shef.ac.uk/shef2004/conference.htm

David Wild – I533 2006. Page 35

comparative execution times nci subsets 2 2 ghz intel celeron processor
Comparative execution timesNCI subsets, 2.2 GHz Intel Celeron processor

7h 27m

3h 06m

2h 25m

44m

David Wild – I533 2006. Page 36

clustering a 1 million compound dataset on a 2 2 ghz celeron desktop machine
Clustering a 1 million compound dataseton a 2.2 GHz Celeron Desktop Machine

Results from AVIDD clusters & Teragrid coming soon….

* Time for a single run may vary due to different selection of seeds. Runtimes can be shortened e.g. by using a max. number of iterations or a % relocation cutoff.

David Wild – I533 2006. Page 37

divisive kmeans conclusions
Divisive Kmeans: Conclusions
  • Much faster than Ward’s, speed comparable to K-means, suitable for very large datasets (millions)
    • Time requirements approximately O(N log N)
    • Current implementation can cluster 1m compounds in under a week on a low-power desktop PC
    • Cluster 1m compounds in a few hours with a 4-node parallel Linux cluster
  • Better balance of cluster sizes than Wards or Kmeans
  • Visual inspection of clusters suggests better assembly of compound series than other methods
  • Better clustering of actives together than previously-studied methods
  • Memory requirements minimal
  • Experiments using AVIDD cluster and Teragrid forthcoming(50+ nodes)

David Wild – I533 2006. Page 38

visualization interface level tools
Visualization & interface level tools
  • No matter how clever the smarts underneath, the overriding factor in usefulness will be the quality of scientists’ interaction with the system
  • Contextual Design, Interaction Design (Cooper) and Usability Studies have proven effective in designing the right interfaces for the right peoplein chemical informatics [collaboration with HCI?]
  • Possibility of multiple interfaces for different people groups(Cooper’s “primary personas”)
  • Don’t assume the browser interface – email / NLP ?
  • Start with the basics
    • 2D chemical structure drawing (input)
    • Visualization of large numbers of chemical structures in 2D
    • 3D chemical structure visualization
  • Planning on evaluation of NLP, email, RSS, etc. as well asbrowser-based interfaces

David Wild – I533 2006. Page 39

usability of 2d structure drawing tools
Usability of 2D structure drawing tools
  • Key difference between “sequential” and “random” drawers
  • Huge difference in intuitiveness
  • Key factor how badly you can mess things up
  • Marvin Sketch ≈ JME > ChemDraw >> ISIS Draw

David Wild – I533 2006. Page 40

visualization methods for datasets clusters
Visualization methods for datasets & clusters
  • Partitions
    • Spreadsheets
    • Enhanced Spreadsheets
    • 2D or 3D plots
  • Hierarchies
    • Dendograms
    • Tree Maps
    • Hyperbolic Maps

David Wild – I533 2006. Page 41

slide44
VisualiSAR – with a nod to Edward Tufte.

See http://www.daylight.com/meetings/mug99/Wild/Mug99.html

David Wild – I533 2006. Page 44

slide45
Tree Maps – very Tufte-esque

David Wild – I533 2006. Page 45

3d visualization jmol
3D Visualization - JMOL

Open Source, very flexible, works in a web service environment: jmol.sourceforge.net

David Wild – I533 2006. Page 46

conclusions so far
Conclusions so far
  • Effective exploitation of large volumes and diverse sources of chemical information is a critical problem to solve, with a potential huge impact on the drug discovery process
  • Most information needs of chemists and drug discovery scientists are conceptually straightforward, but complex (for them) to implement
  • All of the technology is now in place to implement may of these information need “use-cases”: the four level model using service-oriented architectures together with smart clients look like a neat way of doing this
  • The aggregation and interface levels offer the most challenges
  • In conjunction with grid computing, rapid and effective organization and visualization of large chemical datasets is feasible in a web service environment
  • Some pieces are missing:
    • Chemical structure search of journals (wait for InChI)
    • Automated patent searching
    • Effective dataset organization
    • Effective interfaces, especially visualization of large numbers of 2D structures(we’re working on it!)

David Wild – I533 2006. Page 47

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