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Grids for Chemical Informatics

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Grids for Chemical Informatics Chemistry, IU Bloomington Oct. 21 2005 Geoffrey Fox Computer Science, Informatics, Physics Pervasive Technology Laboratories – PowerPoint PPT presentation

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Title: Grids for Chemical Informatics


1
Grids for ChemicalInformatics
  • Chemistry, IU Bloomington
  • Oct. 21 2005
  • Geoffrey Fox
  • Computer Science, Informatics, Physics
  • Pervasive Technology Laboratories
  • Indiana University Bloomington IN 47401
  • gcf_at_indiana.edu
  • http//www.infomall.org

2
Why are Grids Important
  • Grids are important for Chemistry because they
    support key functionalities that grow in
    importance as we are deluged with data from
    instruments and simulations
  • Grids provide information access, storage and
    management
  • Grids manage multiple simulations with different
    defining parameters
  • Grids allow complex workflows with data flowing
    between filters
  • Grids define models for portals
  • Grids are built on top of commodity web service
    technology with broad industry support the next
    generation information technology
  • Grids are used in multiple NIH and other life
    science/chemistry projects across the world
    (BIRN, caBIG, myGrid, Comb-e-Chem )

3
Internet Scale Distributed Services
  • Grids use Internet technology and are
    distinguished by managing or organizing sets of
    network connected resources
  • Classic Web allows independent one-to-one access
    to individual resources
  • Grids integrate together and manage multiple
    Internet-connected resources People, Sensors,
    computers, data systems
  • Organization can be explicit as in
  • TeraGrid which federates many supercomputers
  • Deep Web Technologies IR Grid which federates
    multiple data resources
  • CrisisGrid which federates first responders,
    commanders, sensors, GIS, (Tsunami) simulations,
    science/public data
  • Organization can be implicit as in Internet
    resources such as curated databases and
    simulation resources that harmonize a community

4
Different Visions of the Grid
  • Grid just refers to the technologies
  • Or Grids represent the full system/Applications
  • DoDs vision of Network Centric Computing can be
    considered a Grid (linking sensors, warfighters,
    commanders, backend resources) and they are
    building the GiG (Global Information Grid)
  • Utility Computing or X-on-demand (Xdata,
    computer ..) is major computer Industry interest
    in Grids and this is key part of enterprise or
    campus Grids
  • e-Science or Cyberinfrastructure are virtual
    organization Grids supporting global distributed
    science (note sensors, instruments are people are
    all distributed
  • Skype (Kazaa) VOIP system is a Peer-to-peer Grid
    (and VRVS/GlobalMMCS like Internet A/V
    conferencing are Collaboration Grids)
  • Commercial 3G Cell-phones and DoD ad-hoc network
    initiative are forming mobile Grids

5
Types of Computing Grids
  • Running Pleasing Parallel Jobs as in United
    Devices, Entropia (Desktop Grid) cycle stealing
    systems
  • Can be managed (inside the enterprise as in
    Condor) or more informal (as in SETI_at_Home)
  • Computing-on-demand in Industry where jobs
    spawned are perhaps very large (SAP, Oracle )
  • Support distributed file systems as in Legion
    (Avaki), Globus with (web-enhanced) UNIX
    programming paradigm
  • Particle Physics will run some 30,000
    simultaneous jobs
  • Distributed Simulation HLA/RTI style Grids
  • Linking Supercomputers as in TeraGrid
  • Pipelined applications linking data/instruments,
    compute, visualization
  • Seamless Access where Grid portals allow one to
    choose one of multiple resources with a common
    interfaces
  • Parallel Computing typically NOT suited for a
    Grid (latency)

6
Analysis and Visualization
Large Disks
Old Style Metacomputing Grid
Large Scale Parallel Computers
Original Spread a single large Problem over
multiple supercomputers Now-1 Control
multiple smallish jobs each on independent
Computers Now-2 Choose which of a few
supercomputers to use
7
Towards an International Compute Grid
Infrastructure
UK NGS
Leeds
Manchester
Starlight (Chicago)
US TeraGrid
Netherlight (Amsterdam)
Oxford
RAL
SDSC
NCSA
PSC
UCL
UKLight
SC05
Local laptops in Seattle and UK
All sites connected by production network (not
all shown)
Computation
Steering clients
Network PoP
Service Registry
8
Information/Knowledge Grids
  • Distributed (10s to 1000s) of data sources
    (instruments, file systems, curated databases )
  • Data Deluge 1 (now) to 100s petabytes/year
    (2012)
  • Moores law for Sensors
  • Possible filters assigned dynamically (on-demand)
  • Run image processing algorithm on telescope image
  • Run Gene sequencing algorithm on compiled data
  • Needs decision support front end with what-if
    simulations
  • Metadata (provenance) critical to annotate data
  • Integrate across experiments as in
    multi-wavelength astronomy

Data Deluge comes from pixels/year available
9
Data Deluged Science
  • Now particle physics will get 100 petabytes from
    CERN using around 30,000 CPUs simultaneously
    24X7
  • Exponential growth in data and compare to
  • The Bible 5 Megabytes
  • Annual refereed papers 1 Terabyte
  • Library of Congress 20 Terabytes
  • Internet Archive (1996 2002) 100 Terabytes
  • Weather, climate, solid earth (EarthScope)
  • Bioinformatics curated databases (Biocomplexity
    only 1000s of data points at present)
  • Virtual Observatory and SkyServer in Astronomy
  • Environmental Sensor nets
  • In the past, HPCC community worried about data in
    the form of parallel I/O or MPI-IO, but we didnt
    consider it as an enabler of new science and new
    ways of computing
  • Data assimilation was not central to HPCC
  • DoE ASCI set up because didnt want test data!

10
Virtual Observatory Astronomy GridIntegrate
Experiments
Radio
Far-Infrared
Visible
Dust Map
Visible X-ray
Galaxy Density Map
11
International Virtual Observatory Alliance
  • Reached international agreements on Astronomical
    Data Query Language, VOTable 1.1, UCD 1,
    Resource Metadata Schema
  • Image Access Protocol, Spectral Access Protocol
    and Spectral Data Model, Space-Time Coordinates
    definitions and schema
  • Interoperable registries by Jan 2005 (NVO,
    AstroGrid, AVO, JVO) using OAI publishing and
    harvesting
  • So each Community of Interest builds data AND
    service standards that build on GS- and WS-

12
myGrid Project
  • Imminent deluge of data
  • Highly heterogeneous
  • Highly complex and inter-related
  • Convergence of data and literature archives

13
The Williams Workflows
A
B
C
A Identification of overlapping sequence B
Characterisation of nucleotide sequence C
Characterisation of protein sequence
14
Web services
  • Web Services build loosely-coupled, distributed
    applications, (wrapping existing codes and
    databases) based on the SOA (service oriented
    architecture) principles.
  • Web Services interact by exchanging messages in
    SOAP format
  • The contracts for the message exchanges that
    implement those interactions are described via
    WSDL interfaces.

15
A typical Web Service
  • In principle, services can be in any language
    (Fortran .. Java .. Perl .. Python) and the
    interfaces can be method calls, Java RMI
    Messages, CGI Web invocations, totally compiled
    away (inlining)
  • The simplest implementations involve XML messages
    (SOAP) and programs written in net friendly
    languages like Java and Python

PaymentCredit Card
Web Services
WSDL interfaces
Warehouse Shipping control
WSDL interfaces
Web Services
16
Two-level Programming I
  • The Web Service (Grid) paradigm implicitly
    assumes a two-level Programming Model
  • We make a Service (same as a distributed object
    or computer program running on a remote
    computer) using conventional technologies
  • C Java or Fortran Monte Carlo module
  • Data streaming from a sensor or Satellite
  • Specialized (JDBC) database access
  • Such services accept and produce data from users
    files and databases
  • The Grid is built by coordinating such services
    assuming we have solved problem of programming
    the service

17
Two-level Programming II
  • The Grid is discussing the composition of
    distributed services with the runtime interfaces
    to Grid as opposed to UNIX pipes/data streams
  • Familiar from use of UNIX Shell, PERL or Python
    scripts to produce real applications from core
    programs
  • Such interpretative environments are the single
    processor analog of Grid Programming
  • Some projects like GrADS from Rice University are
    looking at integration between service and
    composition levels but dominant effort looks at
    each level separately

18
RepositoriesFederated Databases
Streaming Data
Sensors
Database
Sensor Grid
Database Grid
Research
Education
SERVOGrid
Compute Grid
Customization Services From Researchto Education
Data FilterServices
ResearchSimulations
Analysis and VisualizationPortal
EducationGrid Computer Farm
Grid of Grids Research Grid and Education Grid
19
SERVOGrid Requirements
  • Seamless Access to Data repositories and large
    scale computers
  • Integration of multiple data sources including
    sensors, databases, file systems with analysis
    system
  • Including filtered OGSA-DAI (Grid database
    access)
  • Rich meta-data generation and access with
    SERVOGrid specific Schema extending openGIS
    (Geography as a Web service) standards and using
    Semantic Grid
  • Portals with component model for user interfaces
    and web control of all capabilities
  • Collaboration to support world-wide work
  • Basic Grid tools workflow and notification
  • NOT metacomputing

20
SERVOGrid Portal Screen Shots
21
Earthquake Grid
DoD NCOW Grid


CoI Specific Grids/Services
Earthquake Data Simulation Service ServoIS
C2 (JBI CEE etc.) NCOW-IS Services
7 Portals
Compute Grid
Information Grid
Sensor Grid
6 Collaboration Grid
GIS Grid
9 Application Services
10 Policy (ECS)
8 Data Access/Storage
11 Metadata
4 Discovery
Core Low Level Grid Services
2 Security
5 Mediation
3 Messaging
1 Management
Physical Network
n Service refers to core services identified by
DoD CoI Community of Interest GIS
Geographical Information System
22
BioInformatics Grid
Chemical Informatics Grid
Sequencing Tools Biocomplexity Simulations BIS


Domain Specific Grids/Services
HTS Tools Quantum CalculationsCIS
7 Portals
Compute Grid
Information Grid
Instrument Grid
6 Collaboration Grid
MIS Grid
9 Application Services
10 Policy
8 Data Access/Storage
11 Metadata
4 Discovery
Core Low Level Grid Services
2 Security
5 Workflow
3 Messaging
1 Management
Physical Network
M(B,C)IS Molecular (Bio, Chem) Information System
23
GIS Grid with WMS, WFS, data sources and GML
ltgmlfeatureMembergt ltfaultgt ltnamegt
Northridge2 lt/namegt ltsegmentgt Northridge2
lt/segmentgt ltauthorgt Wald D. J.lt/authorgt
ltgmllineStringPropertygt
ltgmlLineString srsName"null"gt
ltgmlcoordinatesgt -118.72,34.243
-118.591,34.176 lt/gmlcoordinatesgt
lt/gmlLineStringgt lt/gmllineStringPropertygt
lt/faultgt lt/gmlfeatureMembergt
GML becomes CML, CellML, SBML
24
Electric Power and Natural Gas data from LANL
Interdependent Critical Infrastructure Simulations
Zoom-in
Zoom-out
FeatureInfo mode
Measure distance mode
Clear Distance
Drag and Drop mode
Refresh to initial map
25
Integrating Archived Web Feature Services and
Google Maps
Google maps can be integrated with Web Feature
Service Archives to filter and browse seismic
records.
26
What is Happening?
  • Grid ideas are being developed in (at least) four
    communities
  • Web Service W3C, OASIS, (DMTF)
  • Grid Forum (High Performance Computing,
    e-Science)
  • Enterprise Grid Alliance (Commercial Grid Forum
    with a near term focus)
  • Service Standards are being debated
  • Grid Operational Infrastructure is being deployed
  • Grid Architecture and core software being
    developed
  • Apache has several important projects as do
    academia large and small companies
  • Particular System Services are being developed
    centrally OGSA or GS- framework for this in
    GGF WS- for OASIS/W3C/Microsoft-IBM
  • Lots of fields are setting domain specific
    standards and building domain specific services
  • USA started but now Europe is probably in the
    lead and Asia will soon catch USA if momentum
    (roughly zero for USA) continues

27
The Grid and Web Service Institutional Hierarchy
OGSA GS-and some WS- GGF/W3C/.
WS- fromOASIS/W3C/Industry
Apache Axis.NET etc.
Must set standards to get interoperability
28
Location of software for Grid Projects in
Community Grids Laboratory
  • htpp//www.naradabrokering.org provides Web
    service (and JMS) compliant distributed
    publish-subscribe messaging (software overlay
    network)
  • htpp//www.globlmmcs.org is a service oriented
    (Grid) collaboration environment (audio-video
    conferencing)
  • http//www.crisisgrid.org is an OGC (open
    geospatial consortium) Geographical Information
    System (GIS) compliant GIS and Sensor Grid (with
    POLIS center)
  • http//www.opengrids.org has WS-Context, Extended
    UDDI etc.
  • The work is still in progress but NaradaBrokering
    is quite mature
  • All software is open source and freely available

29
Project Goals
  • Establish Requirements from stakeholders
  • Research
  • Pharmaceutical Industry
  • Government
  • Consider educational implications
  • e-Science v Bio/Chem/Molecular Informatics
  • Consider other national and international
    projects to ensure we either lead or use best
    practice
  • Design a Grid architecture and staged
    implementation
  • Start pilot projects led by Chemistry/Chemical
    Informatics
  • Evaluate and iterate
  • Design and implement ?(Chem, Life Science,
    Science, Molecular) Informatics educational
    program that will attract students
  • Write winning center grant in 2006-7

30
Web Services Introduction
  • What are Web Services?
  • A distributed invocation system built on Grid
    computing
  • Independent of platform and programming language
  • Built on existing Web standards
  • A service oriented architecture with
  • Interfaces based on Internet protocols
  • Messages in XML (except for binary data
    attachments)

31
Web Services Introduction
  • A web-based architecture providing for
    interoperability among resources
  • Centralized service registry
  • Solves problems associated with finding, using,
    and combining online resources
  • Employ standard Internet protocols for
  • Communication with resources
  • Automated discovery using centralized registries
  • Communicate with devices, people, and each other
    with the protocols and computer languages

32
Service Oriented Architecture (SOA)
  • Goal is to achieve loose coupling among
    interacting software agents
  • Define service a unit of work done by a service
    provider to achieve desired end results for a
    service consumer
  • Both provider and consumer are roles played by
    software agents on behalf of their owners.

33
How does SOA work?
  • Two architectural constraints are employed
  • Small set of simple and ubiquitous interfaces to
    all participating software agents
  • Descriptive messages constrained by an extensible
    schema delivered through the interfaces

34
Web Services Architectures
  • Individual services are registered globally
  • Broken down into individual services with inputs
    and outputs specified
  • Services are published
  • Services are requested
  • Open registry, publishing, and requesting

35
Service-Oriented Architecture
  • From Curcin et al. DDT, 2005, 10(12),867

36
Web Services for Science
  • Invisible Services, Semantic Web, and Grid
  • Easy-to-use tools for any scientist
  • High throughput, resource intensive computing
    done for low cost/resources
  • Shared community
  • Collaborations between labs and fields
  • Shared data
  • Shared tools

37
e-Science and the Grid 1
  • e-Science Major UK Program
  • global collaboration in key areas of science and
    the next generation of infrastructure that will
    enable it
  • reflects growing importance of international
    laboratories, satellites and sensors and their
    integrated analysis by distributed teams
  • total investment of some 200M over the five-year
    period from 2001 to 2006
  • CyberInfrastructure the analogous US initiative
  • Grid Technology supports e-Science
    Cyberinfrastructure

38
Basic ArchitecturesServlets/CGI and Web Services
Browser
Browser
GUI Client
Web Server
HTTP GET/POST
WSDL
SOAP
Web Server
WSDL
Web Server
WSDL
WSDL
SOAP
JDBC
JDBC
DB or MPI Appl.
DB or MPI Appl.
39
Importance of Web Services
  • Building a true science community
  • Enabling interoperability between tools and the
    integration of data
  • Less time coding, more time for science
  • Change the way scientists work by achieving new
    levels of integration

40
When To Use Web Services?
  • Applications do not have severe restrictions on
    reliability and speed.
  • Two or more organizations need to cooperate.
  • One needs to write an application that uses
    anothers service.
  • Services can be upgraded independently of
    clients.
  • Services can be easily expressed with simple
    request/response semantics and simple state.

41
Web Services Benefits
  • Web services provide a clean separation between a
    capability and its user interface.
  • Increase in productivity
  • Increase in flexibility
  • Rapid return on investment
  • Integration across multiple applications

42
Web Services Advantages
  • Output in human- and computer-readable formats
  • I/O formats based on standard Internet protocols
  • Resources accessible server to server allow
    automated I/O
  • Integration based on specific services you
    select services or data needed without
    downloading the entire data set

43
Web Services Advantages
  • Description protocols provide details of service
    provided and interface components
  • Semantic Web standards increase efficiency
  • Use a central registry and standardized
    description of services
  • Quality and status of the information is
    dynamically available

44
Web Services Drawbacks
  • Based on new technologies
  • Time and commitment required to learn
  • Standards still in a state of rapid flux
  • Issues with quality of data, (and for chemistry,
    quantity of open data), security, and privacy

45
Components of Web Services
  • Protocols
  • SOAP
  • WSDL
  • UDDI
  • XML as a basis for the protocols
  • Ontologies
  • OWL Ontology Web Language
  • Semantic Web

46
Components of the Semantic Web for Chemistry
  • XML eXtensible Markup Language
  • RDF Resource Description Framework
  • RSS Rich Site Summary
  • Dublin Core allows metadata-based newsfeeds
  • OWL for ontologies
  • BPEL4WS for workflow and web services
  • Murray-Rust et al. Org. Biomol. Chem. 2004, 2,
    3192-3203.

47
SOAP Simple Object Access Protocol
  • Flexible protocol to communicate information
    between server and server or client and server
    using XML
  • Supports Remote Procedure Calls
  • Allows layers (security, authentication,
    transactions) over the basic SOAP elements

48
WSDL Web Service Definition Language
  • Describes a services interface to clients
  • Services register themselves with Web Services
  • WSDL describes how to contact and interact with
    services
  • I/O, operations and messages to aid interaction
    with client

49
WSDL Overview
  • An XML-based Interface Definition Language.
  • You can define the APIs for all of your services
    in WSDL.
  • WSDL docs are broken into five major parts
  • Data definitions (in XML) for custom types
  • Abstract message definitions (request, response)
  • Organization of messages into ports and
    operations (?classes and methods).
  • Protocol bindings (to SOAP, for example)
  • Service point locations (URLs)
  • Some interesting features
  • A single WSDL document can describe several
    versions of an interface.
  • A single WSDL doc can describe several related
    services.

50
UDDI Universal Description, Discovery, and
Integration
  • Provides ways for clients and services to
    interact with other services
  • Uses XML
  • Defines the means of access, e.g.,
  • URL
  • E-Mail
  • Defines services hosted by an entity
  • Business-oriented tags
  • Uses SOAP for communicating

51
XML eXtensible Markup Language
  • Allows definitions of types of documents
  • Tags are used to specify components of documents
  • Allows specification of namespaces to
    differentiate between identical tag names
  • Tag names do not provide semantics other than
    simple hierarchical relations

52
XML Overview
  • A language for building languages
  • Basic rules be well formed and be valid
  • Particular XML dialects are defined by XML
    schemas.
  • XML itself is defined by its own schema.
  • Extensible via namespaces
  • Many non-Web services dialects
  • RDF, SVG, GML, CML, XForms, XHTML
  • Many basic tools available parsers, XPath and
    XQuery for searching/querying, etc.

53
XML and Web services
  • XML lends itself to distributed computing
  • Its just a data description.
  • Platform, programming language independent
  • Web Services Description Language (WSDL)
  • Describes how to invoke a service
  • Can bind to SOAP, other protocols for actual
    invocation
  • Simple Object Access Protocol (SOAP)
  • Wire protocol extension for conveying RPC calls
  • Can be carried over HTTP, SMTP

54
OWL Web Ontology Language
  • Builds on RDF and RDFS and adds a means for
    richer descriptions of properties and classes
  • Disjoint classes
  • Cardinality of classes
  • Characteristics of relations, like symmetry

55
Standards for Web Services
  • Business Process Execution Language for Web
    Services (BPEL4WS)
  • Ontology Web Language Semantics (OWL-S)
  • Web Service Modeling Ontology (WSMO)

56
Standards Setting Boards
  • OASIS Organization for Advancement of Structured
    Information Standards
  • ebXML e-business XML
  • UDDI Universal Description, Discovery and
    Integration
  • Global Grid Forum
  • community of users, developers, and vendors
    leading the global standardization effort for
    grid computing

57
Standards Setting Boards
  • W3C World Wide Web Consortium
  • OWL Ontology Web Language
  • RDF/RDFS Resource Description Framework/Schema
  • SOAP Simple Object Access Protocol
  • URI/URL/URN Universal Resource
    Identifier/Locator/Name
  • WSDL Web Service Definition Language
  • XML eXtensible Markup Language

58
SWWS Semantic Web-Enabled Web Services
  • Main objectives
  • Provide a comprehensive Web Service description
    framework
  • Define a Web Service discovery framework
  • Provide a scalable Web Service mediation
    middleware
  • A program of the European Commission to run
    2002-2005
  • http//swws.semanticweb.org

59
Web Services Integration Projects Biosciences
  • myGrid
  • http//www.mygrid.org.uk/
  • BIOPIPE
  • http//biopipe.org/
  • BioMOBY
  • http//biomoby.org/

60
Web Services for Chemistry Problems
  • Performance and scalability
  • Proprietary data
  • Competition from high-performance desktop
    applications
  • -- Geoff Hutchison, its a puzzle blog,
    2005-01-05
  • ALSO
  • Lack of a substantial body of trustworthy Open
    Access databases
  • Non-standard chemical data formats (over 40 in
    regular use and requiring normalization to one
    another)

61
Missing Ingredients in Chemistry
  • Chemical communities to assemble Open Access
    databases
  • Well-defined quality assurance procedures
    performed by distributed peer-review systems
  • Software underlying the databases needs to be
    open source.

62
Chemistry Databases on the Web
  • Marc Nicklaus lists 37 databases as of October
    2001
  • Must have structure searching and at least 100
    molecules
  • http//cactus.nci.nih.gov/ncidb2/chem_www.html
  • SoaringBears List has 15 databases
  • http//geocities.com/soaringbear/biomed/chem.html

63
Institutional Repositories
  • NARSTO Quality Systems Science Center
  • http//cdiac.esd.ornl.gov/programs/NARSTO/
  • Pollutant species in the troposphere over North
    America
  • Part of the Carbon Dioxide Information Analysis
    Center at ORNL
  • NARSTO Data and Information Sharing Tool
  • http//mercury.ornl.gov/narsto/

64
Public Data Repositories
  • Developmental Therapeutics Program/NCI
  • Some assay data for download
  • Structures for over 200,000 compounds
  • http//dtp.nci.nih.gov/docs/dtp_search.html
  • Zinc and other screening databases
  • NIST computational chemistry database
  • Environmental fate and exposure databases

65
Other Public Repositories 1
  • ChemExper Chemical Directory
  • gt 200,000 substances gt 10,000 IR spectra
  • http//chemexper.com/
  • HIC-Up Hetero-Compound Identification Centre
    Uppsala
  • 5384 substances as of 1/15/05
  • http//xray.bmc.uu.se/hicup/
  • Chemicals with Pharmaceutical Activity a 3D
    Structural Database
  • 400 3D structures
  • http//www.chem.ox.ac.uk/mom/chemical-database/

66
Other Public Repositories 2
  • Cheminformatics.org
  • 41 data sets in 9 categories as of 8/18/05
  • http//www.cheminformatics.org/
  • WebReactions
  • http//webreactions.net/

67
Other Public Repositories 3
  • MolTable
  • http//www.moltable.org/
  • MatWeb Materials Property Data
  • http//www.matweb.com/index.asp?ckck1
  • Spectral Database for Organic Compounds (SDBS)
  • Over 32,000 compounds
  • Has EI-MS, FT-IR, 1H NMR, 13C NMR, Raman, ESR
  • http//www.aist.go.jp/RIODB/SDBS/cgi-bin/cre_index
    .cgi
  • NMRShiftDB (Christoph Steinbeck)
  • 14,753 structures as of 8/19/05
  • Features peer-reviewed submission of data sets
  • http//www.nmrshiftdb.org/

68
Other Public RepositoriesCommercial Teasers
  • FTIRsearch.com (Thermo Electron)
  • Demo file of 575 spectra from 87,000 in the full
    database
  • https//ftirsearch.com/default3.htm
  • ChemACX
  • 30 of gt350 suppliers catalog data
  • http//chemacx.cambridgesoft.com/chemacx/index.asp
  • Sunset Molecular Discovery, LLC
  • Wombat (World of Molecular BioAcTivity)
  • 117,007 entries with over 230,000 biological
    activities
  • Wombat PK
  • Database for Clinical Pharmacokinetics 643
    substances with 4668 measurements
  • Three sample files from Wombat containing 341
    Histamine-1 receptor antagonists
  • http//www.sunsetmolecular.com/

69
BlueObelisk.org
  • A group of chemists, programmers, and
    informaticians working collaboratively on
    projects such as
  • Chemistry Development Kit (CDK)
  • JChemPaint
  • Jmol
  • JUMBO
  • NMRShiftDB
  • Octet
  • Open Babel
  • QSAR
  • World Wide Molecular Matrix (WWMM)

70
Indiana University Existing Projects
  • System for the Integration of Bioinformatics
    Services (SIBIOS)
  • http//sibios.engr.iupui.edu
  • PlatCom A Platform for Computational Comparative
    Genomics
  • http//bio.informatics.indiana.edu/sunkim/Platcom/
  • Reciprocal Net
  • http//www.reciprocalnet.org/index.html

71
Indiana University Planned Projects
  • Design of a Grid-based distributed data
    architecture
  • Development of tools for HTS data analysis and
    virtual screening
  • Database for quantum mechanical simulation data
  • Chemical prototype projects
  • Novel routes to enzymatic reaction mechanisms
  • Mechanism-based drug design
  • Data-inquiry-based development of new methods in
    natural product synthesis

72
Web Services Future
  • Depends on
  • Adoption of standards
  • Incorporation of WS in current and newly
    developed applications
  • Security, privacy, quality of data issues
  • Development of WS tools and resources for
    e-Science
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