From ca350a4652d35911d695d1ad21624245dac83d00 Mon Sep 17 00:00:00 2001 From: root Date: Mon, 11 Jul 2016 13:09:16 +0200 Subject: add nano-lazar to software list, add Dublin slides --- public/presentations/opentox-dublin/.api.rst.swp | Bin 0 -> 20480 bytes public/presentations/opentox-dublin/api.html | 512 +++++++++++++++++++ public/presentations/opentox-dublin/api.rst | 143 ++++++ public/presentations/opentox-dublin/index.html | 505 +++++++++++++++++++ public/presentations/opentox-dublin/index.rst | 146 ++++++ public/presentations/opentox-dublin/logo.png | Bin 0 -> 25812 bytes .../opentox-dublin/ui/default/blank.gif | Bin 0 -> 49 bytes .../opentox-dublin/ui/default/framing.css | 25 + .../opentox-dublin/ui/default/iepngfix.htc | 42 ++ .../opentox-dublin/ui/default/opera.css | 8 + .../opentox-dublin/ui/default/outline.css | 16 + .../opentox-dublin/ui/default/pretty.css | 120 +++++ .../opentox-dublin/ui/default/print.css | 24 + .../opentox-dublin/ui/default/s5-core.css | 11 + .../opentox-dublin/ui/default/slides.css | 10 + .../opentox-dublin/ui/default/slides.js | 558 +++++++++++++++++++++ .../opentox-dublin/ui/small-white/blank.gif | Bin 0 -> 49 bytes .../opentox-dublin/ui/small-white/framing.css | 24 + .../opentox-dublin/ui/small-white/iepngfix.htc | 42 ++ .../opentox-dublin/ui/small-white/opera.css | 8 + .../opentox-dublin/ui/small-white/outline.css | 16 + .../opentox-dublin/ui/small-white/pretty.css | 114 +++++ .../opentox-dublin/ui/small-white/print.css | 24 + .../opentox-dublin/ui/small-white/s5-core.css | 11 + .../opentox-dublin/ui/small-white/slides.css | 10 + .../opentox-dublin/ui/small-white/slides.js | 558 +++++++++++++++++++++ views/software.haml | 8 + 27 files changed, 2935 insertions(+) create mode 100644 public/presentations/opentox-dublin/.api.rst.swp create mode 100644 public/presentations/opentox-dublin/api.html create mode 100644 public/presentations/opentox-dublin/api.rst create mode 100644 public/presentations/opentox-dublin/index.html create mode 100644 public/presentations/opentox-dublin/index.rst create mode 100644 public/presentations/opentox-dublin/logo.png create mode 100644 public/presentations/opentox-dublin/ui/default/blank.gif create mode 100755 public/presentations/opentox-dublin/ui/default/framing.css create mode 100644 public/presentations/opentox-dublin/ui/default/iepngfix.htc create mode 100644 public/presentations/opentox-dublin/ui/default/opera.css create mode 100755 public/presentations/opentox-dublin/ui/default/outline.css create mode 100755 public/presentations/opentox-dublin/ui/default/pretty.css create mode 100755 public/presentations/opentox-dublin/ui/default/print.css create mode 100644 public/presentations/opentox-dublin/ui/default/s5-core.css create mode 100644 public/presentations/opentox-dublin/ui/default/slides.css create mode 100644 public/presentations/opentox-dublin/ui/default/slides.js create mode 100644 public/presentations/opentox-dublin/ui/small-white/blank.gif create mode 100644 public/presentations/opentox-dublin/ui/small-white/framing.css create mode 100755 public/presentations/opentox-dublin/ui/small-white/iepngfix.htc create mode 100755 public/presentations/opentox-dublin/ui/small-white/opera.css create mode 100644 public/presentations/opentox-dublin/ui/small-white/outline.css create mode 100644 public/presentations/opentox-dublin/ui/small-white/pretty.css create mode 100644 public/presentations/opentox-dublin/ui/small-white/print.css create mode 100644 public/presentations/opentox-dublin/ui/small-white/s5-core.css create mode 100644 public/presentations/opentox-dublin/ui/small-white/slides.css create mode 100644 public/presentations/opentox-dublin/ui/small-white/slides.js diff --git a/public/presentations/opentox-dublin/.api.rst.swp b/public/presentations/opentox-dublin/.api.rst.swp new file mode 100644 index 0000000..296cb5b Binary files /dev/null and b/public/presentations/opentox-dublin/.api.rst.swp differ diff --git a/public/presentations/opentox-dublin/api.html b/public/presentations/opentox-dublin/api.html new file mode 100644 index 0000000..5a386a8 --- /dev/null +++ b/public/presentations/opentox-dublin/api.html @@ -0,0 +1,512 @@ + + + + + + + +OpenTox API Working Group + + + + + + + + + + + + + + +
+
+
+ + +
+
+
+

OpenTox API Working Group

+ + + + + +
+
+

Workshop Objectives

+
+
Capture
+
    +
  • service provider (developer) experiences
    • +
  • service consumer (client) experiences
    • +
+
+
+

Identify open issues

+

Resolve open issues

+

Unify and update API documentation

+
+
+

OpenTox

+

http://opentox.org/dev/apis/api-1.2

+

Focus on predictive toxicology

+

REST interfaces for: Compound, Feature, Dataset, Algorithm, Model, Validation, Report, Ontology, Task, Authentication and Authorisation

+

RDF representation

+
+
+

ToxBank

+

http://api.toxbank.net

+

Extensions for capturing bioassay data

+

Additional objects: Alert, Data, Index, Investigation, Organisation, Project, Protocol, Search, Session, Template, User.

+

RDF representation, ISA-Tab (http://isatab.sourceforge.net/format.html)

+
+
+

eNanoMapper

+

IDEA: http://enanomapper.github.io/API

+

NTUA: http://app.jaqpot.org:8080/jaqpot/swagger

+

IST: https://enm.in-silico.ch/api/dist

+

Extensions for capturing nanomaterial data

+

Additional objects: Bundle, Myaccount, Property, Query, Substance, Substanceowner, Pmml, Bibtex

+

JSON representation

+
+
+

Developer experiences

+
+
+

(De)Serialisation of large datasets/investigations

+
+
    +
  • system/infrastructure limitations (time, memory, database/webserver size limits, ...)
    • +
  • impossible for RDF (performance of RDF parsers/serializers, markup size)
    • +
  • even JSON markup can cause problems
    • +
  • we propose CSV/TSV as data exchange format for datasets
    • +
+
+
+
+

Complexity of the one webservice/class model

+
+
    +
  • code separation, maintenance
    • +
  • performance penalties caused by suboptimal data structures
    • +
  • performance penalties of webservices (data (de)serialisation)
    • +
  • complicated server infrastructure
    • +
+
+
+
+

Communication with external services

+
+
    +
  • ad hoc requests for features that deviate from official API
    • +
  • reliablity/availability of external services
    • +
  • undocumented API details
    • +
  • undocumented/silent API/data format changes
    • +
  • no common strategy for conflict resolution, API or data representation updates
    • +
+
+
+
+

Local service deployment (e.g. for in house services)

+
+
    +
  • installation far from straightforward
    • +
  • management of additional server instances
    • +
  • duplication of functionality, bloat
    • +
  • update strategy
    • +
+
+
+
+

Documentation

+
+
    +
  • scattered/outdated documentation
    • +
  • maintenance +- too many places to consider (error prone) +- ideally autogenerated from code
    • +
  • ideally combined with tests (availability, API coverage, API compliance)
    • +
+
+
+
+

Client experiences

+
+
+

Open issues

+
+
Workflow for
+
    +
  • API unification and updates
    • +
  • issue and conflict reporting/resolution
    • +
+
+
Documentation
+
    +
  • location
    • +
  • format (Swagger, Wiki, ...)
    • +
  • maintenance
    • +
  • link to inventories, tests
    • +
+
+
+

...

+
+ +
+

Next steps

+
+
+ + diff --git a/public/presentations/opentox-dublin/api.rst b/public/presentations/opentox-dublin/api.rst new file mode 100644 index 0000000..2763b50 --- /dev/null +++ b/public/presentations/opentox-dublin/api.rst @@ -0,0 +1,143 @@ +.. |date| date:: + +========================= +OpenTox API Working Group +========================= + +.. :Date: 30 September 2015 + +.. University College Dublin, Dublin, Ireland + +.. https://docs.google.com/document/d/153ip9ll_pzqMphoJ4d608ujd5GuYysZcTDAODsrXsrc/edit + +Workshop Objectives +=================== + +Capture + - service provider (developer) experiences + - service consumer (client) experiences + +Identify open issues + +Resolve open issues + +Unify and update API documentation + +OpenTox +======= + +http://opentox.org/dev/apis/api-1.2 + +Focus on predictive toxicology + +REST interfaces for: Compound, Feature, Dataset, Algorithm, Model, Validation, Report, Ontology, Task, Authentication and Authorisation + +RDF representation + +ToxBank +======= + +http://api.toxbank.net + +Extensions for capturing bioassay data + +Additional objects: Alert, Data, Index, Investigation, Organisation, Project, Protocol, Search, Session, Template, User. + +RDF representation, ISA-Tab (http://isatab.sourceforge.net/format.html) + +eNanoMapper +=========== + +IDEA: http://enanomapper.github.io/API + +NTUA: http://app.jaqpot.org:8080/jaqpot/swagger + +IST: https://enm.in-silico.ch/api/dist + +Extensions for capturing nanomaterial data + +Additional objects: Bundle, Myaccount, Property, Query, Substance, Substanceowner, Pmml, Bibtex + +JSON representation + + +Developer experiences +===================== + +(De)Serialisation of large datasets/investigations +================================================== + + - system/infrastructure limitations (time, memory, database/webserver size limits, ...) + - impossible for RDF (performance of RDF parsers/serializers, markup size) + - even JSON markup can cause problems + - we propose CSV/TSV as data exchange format for datasets + +Complexity of the one webservice/class model +============================================ + + - code separation, maintenance + - performance penalties caused by suboptimal data structures + - performance penalties of webservices (data (de)serialisation) + - complicated server infrastructure + +Communication with external services +==================================== + + - ad hoc requests for features that deviate from official API + - reliablity/availability of external services + - undocumented API details + - undocumented/silent API/data format changes + - no common strategy for conflict resolution, API or data representation updates + +Local service deployment (e.g. for in house services) +===================================================== + + - installation far from straightforward + - management of additional server instances + - duplication of functionality, bloat + - update strategy + +Documentation +============= + + - scattered/outdated documentation + - maintenance + - too many places to consider (error prone) + - ideally autogenerated from code + - ideally combined with tests (availability, API coverage, API compliance) + +Client experiences +================== + +Open issues +=========== + +Workflow for + - API unification and updates + - issue and conflict reporting/resolution + +Documentation + - location + - format (Swagger, Wiki, ...) + - maintenance + - link to inventories, tests + +... + +OpenTox APIs +============ + +http://opentox.org/dev/apis/api-1.2 + +http://api.toxbank.net + +http://enanomapper.github.io/API + +http://app.jaqpot.org:8080/jaqpot/swagger + +https://enm.in-silico.ch/api/dist + + +Next steps +========== + diff --git a/public/presentations/opentox-dublin/index.html b/public/presentations/opentox-dublin/index.html new file mode 100644 index 0000000..e2ef48f --- /dev/null +++ b/public/presentations/opentox-dublin/index.html @@ -0,0 +1,505 @@ + + + + + + + +Extending OpenTox to Nano Safety with eNanoMapper + + + + + + + + + + + + + + +
+
+
+ + +
+
+
+

Extending OpenTox to Nano Safety with eNanoMapper

+ +

Christoph Helma

+

in silico toxicology gmbh

+logo.png + +
+
+

Basic idea

+

Webservices as building blocks for computational toxicology

+
+
    +
  • avoid reinventing the wheel
    • +
  • reuse existing components
    • +
  • rapid prototyping
    • +
  • interoperability
    • +
  • uses semantic web technologies
    • +
+
+
+
+

Application programming interface (API)

+
+
Request messages:
+
    +
  • Representational state transfer (REST, based on HTTP messages)
    • +
+
+
Data exchange:
+
    +
  • Structure: object dependent
    • +
  • Format: Resource Description Framework (RDF), JavaScript Object Notation (JSON)
    • +
+
+
+
+
+

OpenTox

+

Focus on predictive toxicology

+

Main objects: Compound, Feature, Dataset, Algorithm, Model, Validation

+

Helper objects: Task, Authentication and Authorisation, Report, Ontology

+

Data format: RDF

+

http://opentox.org/dev/apis/api-1.2

+
+
+

ToxBank

+

Extensions for capturing bioassay data

+

Main addition: Investigation (description of biological experiments)

+

Helper objects: Organisation, Project, Protocol, Search, Session, Template, User, Alert, Data, Index

+

Data format: RDF, ISA-Tab

+

http://api.toxbank.net

+
+
+

eNanoMapper

+

Extensions for capturing nanomaterial data

+

Main addition: Substance (characterisation of nanoparticles)

+

Helper objects: Bundle (datasets of substances), Property, Query, Substanceowner, Myaccount, Pmml, Bibtex

+

Data format: JSON

+
+ +
+

Technical problems

+
    +
  • (De)Serialisation of large datasets/investigations
    • +
  • Reliability/availability/compatibility of external services
    • +
  • Local service deployment (e.g. for in house services)
    • +
+
+
+

Documentation problems

+
    +
  • Scattered/outdated documentation
    • +
  • Difficult to maintain for developers (no suitable cross-platform solution for code-based documentation)
    • +
  • Limitations of documentation platforms (e.g. SWAGGER) to document important details
    • +
+
+
+

API problems

+
    +
  • Lack of orthogonality (large number of partially redundant helper objects)
    • +
  • Ad hoc extensions of individual developers
    • +
  • Undocumented/silent API/data format changes
    • +
+
+
+

Coordination problems

+
    +
  • Individual API changes may be necessary and justified
    • +
  • Conflict resolution works one to one, but leaves out other developers (and consistency)
    • +
  • No common strategy for conflict resolution and API updates
    • +
  • Very limited developer base for testing and feedback
    • +
+
+
+

API features

+
    +
  • Covers arbitrary biological and chemical experiments (via ToxBank investigations)
      +
    • storage/search/retrieval of data and metadata (experimental layouts)
      • +
    • generic structure for all types of experiments (including -omics)
      • +
    • includes preprocessing, data analysis and modelling steps
      • +
    • protocols for experimental and data analysis steps
      • +
    +
    • +
+
+
+

API features

+
    +
  • Nanomaterial characterisations (via eNM substances)
    • +
  • Datasets (bundles) for data analysis
    • +
  • Algorithms for data analysis, modelling, descriptor calculation, ...
    • +
  • Models for model predictions
    • +
  • Validation for model validation
    • +
  • User authentication and authorisation
    • +
  • Tasks for long running processes
    • +
  • ...
    • +
+
+ +
+ + diff --git a/public/presentations/opentox-dublin/index.rst b/public/presentations/opentox-dublin/index.rst new file mode 100644 index 0000000..9a5846f --- /dev/null +++ b/public/presentations/opentox-dublin/index.rst @@ -0,0 +1,146 @@ +.. |date| date:: + +============================================================================= +Extending OpenTox to Nano Safety with eNanoMapper +============================================================================= + +.. class:: center + + Christoph Helma + + in silico toxicology gmbh + + .. image:: logo.png + +Basic idea +========== + +Webservices as building blocks for computational toxicology + + - avoid reinventing the wheel + - reuse existing components + - rapid prototyping + - interoperability + - uses semantic web technologies + +Application programming interface (API) +======================================= + +Request messages: + - Representational state transfer (*REST*, based on HTTP messages) + +Data exchange: + - Structure: object dependent + - Format: Resource Description Framework (*RDF*), JavaScript Object Notation (*JSON*) + +OpenTox +======= + +*Focus on predictive toxicology* + +Main objects: Compound, Feature, Dataset, Algorithm, Model, Validation + +Helper objects: Task, Authentication and Authorisation, Report, Ontology + +Data format: RDF + +http://opentox.org/dev/apis/api-1.2 + +ToxBank +======= + +*Extensions for capturing bioassay data* + +Main addition: Investigation (description of biological experiments) + +Helper objects: Organisation, Project, Protocol, Search, Session, Template, User, Alert, Data, Index + +Data format: RDF, ISA-Tab + +http://api.toxbank.net + +eNanoMapper +=========== + +*Extensions for capturing nanomaterial data* + +Main addition: Substance (characterisation of nanoparticles) + +Helper objects: Bundle (datasets of substances), Property, Query, Substanceowner, Myaccount, Pmml, Bibtex + +Data format: JSON + +eNanoMapper APIs +================ + +IDEA: http://enanomapper.github.io/API + +NTUA: http://app.jaqpot.org:8080/jaqpot/swagger + +IST: https://enm.in-silico.ch/api/dist + +Technical problems +================== + +- (De)Serialisation of large datasets/investigations +- Reliability/availability/compatibility of external services +- Local service deployment (e.g. for in house services) + +Documentation problems +====================== + +- Scattered/outdated documentation +- Difficult to maintain for developers (no suitable cross-platform solution for code-based documentation) +- Limitations of documentation platforms (e.g. SWAGGER) to document important details + +API problems +============ + +- Lack of orthogonality (large number of partially redundant helper objects) +- Ad hoc extensions of individual developers +- Undocumented/silent API/data format changes + +Coordination problems +===================== + +- Individual API changes may be necessary and justified +- Conflict resolution works one to one, but leaves out other developers (and consistency) +- No common strategy for conflict resolution and API updates +- Very limited developer base for testing and feedback + +API features +============ + +- Covers arbitrary biological and chemical experiments (via ToxBank investigations) + + - storage/search/retrieval of data *and* metadata (experimental layouts) + - generic structure for *all* types of experiments (including -omics) + - includes preprocessing, data analysis and modelling steps + - protocols for experimental and data analysis steps + +API features +============ + +- Nanomaterial characterisations (via eNM substances) +- Datasets (bundles) for data analysis +- Algorithms for data analysis, modelling, descriptor calculation, ... +- Models for model predictions +- Validation for model validation + +- User authentication and authorisation +- Tasks for long running processes +- ... + +OpenTox/ToxBank/eNanoMapper APIs +================================ + +http://opentox.org/dev/apis/api-1.2 + +http://api.toxbank.net + +http://enanomapper.github.io/API + +http://app.jaqpot.org:8080/jaqpot/swagger + +https://enm.in-silico.ch/api/dist + diff --git a/public/presentations/opentox-dublin/logo.png b/public/presentations/opentox-dublin/logo.png new file mode 100644 index 0000000..4a3621a Binary files /dev/null and b/public/presentations/opentox-dublin/logo.png differ diff --git a/public/presentations/opentox-dublin/ui/default/blank.gif b/public/presentations/opentox-dublin/ui/default/blank.gif new file mode 100644 index 0000000..75b945d Binary files /dev/null and b/public/presentations/opentox-dublin/ui/default/blank.gif differ diff --git a/public/presentations/opentox-dublin/ui/default/framing.css b/public/presentations/opentox-dublin/ui/default/framing.css new file mode 100755 index 0000000..c4727f3 --- /dev/null +++ b/public/presentations/opentox-dublin/ui/default/framing.css @@ -0,0 +1,25 @@ +/* This file has been placed in the public domain. */ +/* The following styles size, 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margin: 0 auto;} +.slide tt {font-size: 90%;} + +div#header, div#footer {background: #005; color: #AAB; font-family: sans-serif;} +/* background: #005 url(bodybg.gif) -16px 0 no-repeat; */ +div#footer {font-size: 0.5em; font-weight: bold; padding: 1em 0;} +#footer h1 {display: block; padding: 0 1em;} +#footer h2 {display: block; padding: 0.8em 1em 0;} + +.slide {font-size: 1.2em;} +.slide h1 {position: absolute; top: 0.45em; z-index: 1; + margin: 0; padding-left: 0.7em; white-space: nowrap; + font: bold 150% sans-serif; color: #DDE; background: #005;} +.slide h2 {font: bold 120%/1em sans-serif; padding-top: 0.5em;} +.slide h3 {font: bold 100% sans-serif; padding-top: 0.5em;} +h1 abbr {font-variant: small-caps;} + +div#controls {position: absolute; left: 50%; bottom: 0; + width: 50%; text-align: right; font: bold 0.9em sans-serif;} +html>body div#controls {position: fixed; padding: 0 0 1em 0; top: auto;} +div#controls form {position: absolute; bottom: 0; right: 0; width: 100%; + margin: 0; padding: 0;} +#controls #navLinks a {padding: 0; margin: 0 0.5em; + background: #005; border: none; color: #779; cursor: pointer;} +#controls #navList {height: 1em;} +#controls #navList #jumplist {position: absolute; bottom: 0; right: 0; + background: #DDD; color: #227;} + +#currentSlide {text-align: center; font-size: 0.5em; color: #449; + font-family: sans-serif; font-weight: bold;} + +#slide0 {padding-top: 1.5em} +#slide0 h1 {position: static; margin: 1em 0 0; padding: 0; color: #000; + font: bold 2em sans-serif; white-space: normal; background: transparent;} +#slide0 h2 {font: bold italic 1em sans-serif; margin: 0.25em;} +#slide0 h3 {margin-top: 1.5em; font-size: 1.5em;} +#slide0 h4 {margin-top: 0; font-size: 1em;} + +ul.urls {list-style: none; display: inline; margin: 0;} +.urls li {display: inline; margin: 0;} +.external {border-bottom: 1px dotted gray;} +html>body .external {border-bottom: none;} +.external:after {content: " \274F"; font-size: smaller; color: #77B;} + +.incremental, .incremental *, .incremental *:after {visibility: visible; + color: white; border: 0;} +img.incremental {visibility: hidden;} +.slide .current {color: green;} + +.slide-display {display: inline ! important;} + +.huge {font-family: sans-serif; font-weight: bold; font-size: 150%;} +.big {font-family: sans-serif; font-weight: bold; font-size: 120%;} +.small {font-size: 75%;} +.tiny {font-size: 50%;} +.huge tt, .big tt, .small tt, .tiny tt {font-size: 115%;} +.huge pre, .big pre, .small pre, .tiny pre {font-size: 115%;} + +.maroon {color: maroon;} +.red {color: red;} +.magenta {color: magenta;} +.fuchsia {color: fuchsia;} +.pink {color: #FAA;} +.orange {color: orange;} +.yellow {color: yellow;} +.lime {color: lime;} +.green {color: green;} +.olive {color: olive;} +.teal {color: teal;} +.cyan {color: cyan;} +.aqua {color: aqua;} +.blue {color: blue;} +.navy {color: navy;} +.purple {color: purple;} +.black {color: black;} +.gray {color: gray;} +.silver {color: silver;} +.white {color: white;} + +.left {text-align: left ! important;} +.center {text-align: center ! important;} +.right {text-align: right ! important;} + +.animation {position: relative; margin: 1em 0; padding: 0;} +.animation img {position: absolute;} + +/* Docutils-specific overrides */ + +.slide table.docinfo {margin: 1em 0 0.5em 2em;} + +pre.literal-block, pre.doctest-block {background-color: white;} + +tt.docutils {background-color: white;} + +/* diagnostics */ +/* +li:after {content: " [" attr(class) "]"; color: #F88;} +div:before {content: "[" attr(class) "]"; color: #F88;} +*/ diff --git a/public/presentations/opentox-dublin/ui/default/print.css b/public/presentations/opentox-dublin/ui/default/print.css new file mode 100755 index 0000000..9d057cc --- /dev/null +++ b/public/presentations/opentox-dublin/ui/default/print.css @@ -0,0 +1,24 @@ +/* This file has been placed in the public domain. */ +/* The following rule is necessary to have all slides appear in print! + DO NOT REMOVE IT! */ +.slide, ul {page-break-inside: avoid; visibility: visible !important;} +h1 {page-break-after: avoid;} + +body {font-size: 12pt; background: white;} +* {color: black;} + +#slide0 h1 {font-size: 200%; border: none; margin: 0.5em 0 0.25em;} +#slide0 h3 {margin: 0; padding: 0;} +#slide0 h4 {margin: 0 0 0.5em; padding: 0;} +#slide0 {margin-bottom: 3em;} + +#header {display: none;} +#footer h1 {margin: 0; border-bottom: 1px solid; color: gray; + font-style: italic;} +#footer h2, #controls {display: none;} + +.print {display: inline ! important;} + +/* The following rule keeps the layout stuff out of print. + Remove at your own risk! */ +.layout, .layout * {display: none !important;} diff --git a/public/presentations/opentox-dublin/ui/default/s5-core.css b/public/presentations/opentox-dublin/ui/default/s5-core.css new file mode 100644 index 0000000..6965f5e --- /dev/null +++ b/public/presentations/opentox-dublin/ui/default/s5-core.css @@ -0,0 +1,11 @@ +/* This file has been placed in the public domain. */ +/* Do not edit or override these styles! + The system will likely break if you do. */ + +div#header, div#footer, div#controls, .slide {position: absolute;} +html>body div#header, html>body div#footer, + html>body div#controls, html>body .slide {position: fixed;} +.handout {display: none;} +.layout {display: block;} +.slide, .hideme, .incremental {visibility: hidden;} +#slide0 {visibility: visible;} diff --git a/public/presentations/opentox-dublin/ui/default/slides.css b/public/presentations/opentox-dublin/ui/default/slides.css new file mode 100644 index 0000000..82bdc0e --- /dev/null +++ b/public/presentations/opentox-dublin/ui/default/slides.css @@ -0,0 +1,10 @@ +/* This file has been placed in the public domain. */ + +/* required to make the slide show run at all */ +@import url(s5-core.css); + +/* sets basic placement and size of slide components */ +@import url(framing.css); + +/* styles that make the slides look good */ +@import url(pretty.css); diff --git a/public/presentations/opentox-dublin/ui/default/slides.js b/public/presentations/opentox-dublin/ui/default/slides.js new file mode 100644 index 0000000..81e04e5 --- /dev/null +++ b/public/presentations/opentox-dublin/ui/default/slides.js @@ -0,0 +1,558 @@ +// S5 v1.1 slides.js -- released into the Public Domain +// Modified for Docutils (http://docutils.sf.net) by David Goodger +// +// Please see http://www.meyerweb.com/eric/tools/s5/credits.html for +// information about all the wonderful and talented contributors to this code! + +var undef; +var slideCSS = ''; +var snum = 0; +var smax = 1; +var slideIDs = new Array(); +var incpos = 0; +var number = undef; +var s5mode = true; +var defaultView = 'slideshow'; +var controlVis = 'visible'; + +var isIE = navigator.appName == 'Microsoft Internet Explorer' ? 1 : 0; +var isOp = navigator.userAgent.indexOf('Opera') > -1 ? 1 : 0; +var isGe = navigator.userAgent.indexOf('Gecko') > -1 && navigator.userAgent.indexOf('Safari') < 1 ? 1 : 0; + +function hasClass(object, className) { + if (!object.className) return false; + return (object.className.search('(^|\\s)' + className + '(\\s|$)') != -1); +} + +function hasValue(object, value) { + if (!object) return false; + return (object.search('(^|\\s)' + value + '(\\s|$)') != -1); +} + +function removeClass(object,className) { + if (!object) return; + object.className = object.className.replace(new RegExp('(^|\\s)'+className+'(\\s|$)'), RegExp.$1+RegExp.$2); +} + +function addClass(object,className) { + if (!object || hasClass(object, className)) return; + if (object.className) { + object.className += ' '+className; + } else { + object.className = className; + } +} + +function GetElementsWithClassName(elementName,className) { + var allElements = document.getElementsByTagName(elementName); + var elemColl = new Array(); + for (var i = 0; i< allElements.length; i++) { + if (hasClass(allElements[i], className)) { + elemColl[elemColl.length] = allElements[i]; + } + } + return elemColl; +} + +function isParentOrSelf(element, id) { + if (element == null || element.nodeName=='BODY') return false; + else if (element.id == id) return true; + else return isParentOrSelf(element.parentNode, id); +} + +function nodeValue(node) { + var result = ""; + if (node.nodeType == 1) { + var children = node.childNodes; + for (var i = 0; i < children.length; ++i) { + result += nodeValue(children[i]); + } + } + else if (node.nodeType == 3) { + result = node.nodeValue; + } + return(result); +} + +function slideLabel() { + var slideColl = GetElementsWithClassName('*','slide'); + var list = document.getElementById('jumplist'); + smax = slideColl.length; + for (var n = 0; n < smax; n++) { + var obj = slideColl[n]; + + var did = 'slide' + n.toString(); + if (obj.getAttribute('id')) { + slideIDs[n] = obj.getAttribute('id'); + } + else { + obj.setAttribute('id',did); + slideIDs[n] = did; + } + if (isOp) continue; + + var otext = ''; + var menu = obj.firstChild; + if (!menu) continue; // to cope with empty slides + while (menu && menu.nodeType == 3) { + menu = menu.nextSibling; + } + if (!menu) continue; // to cope with slides with only text nodes + + var menunodes = menu.childNodes; + for (var o = 0; o < menunodes.length; o++) { + otext += nodeValue(menunodes[o]); + } + list.options[list.length] = new Option(n + ' : ' + otext, n); + } +} + +function currentSlide() { + var cs; + var footer_nodes; + var vis = 'visible'; + if (document.getElementById) { + cs = document.getElementById('currentSlide'); + footer_nodes = document.getElementById('footer').childNodes; + } else { + cs = document.currentSlide; + footer = document.footer.childNodes; + } + cs.innerHTML = '' + snum + '<\/span> ' + + '\/<\/span> ' + + '' + (smax-1) + '<\/span>'; + if (snum == 0) { + vis = 'hidden'; + } + cs.style.visibility = vis; + for (var i = 0; i < footer_nodes.length; i++) { + if (footer_nodes[i].nodeType == 1) { + footer_nodes[i].style.visibility = vis; + } + } +} + +function go(step) { + if (document.getElementById('slideProj').disabled || step == 0) return; + var jl = document.getElementById('jumplist'); + var cid = slideIDs[snum]; + var ce = document.getElementById(cid); + if (incrementals[snum].length > 0) { + for (var i = 0; i < incrementals[snum].length; i++) { + removeClass(incrementals[snum][i], 'current'); + removeClass(incrementals[snum][i], 'incremental'); + } + } + if (step != 'j') { + snum += step; + lmax = smax - 1; + if (snum > lmax) snum = lmax; + if (snum < 0) snum = 0; + } else + snum = parseInt(jl.value); + var nid = slideIDs[snum]; + var ne = document.getElementById(nid); + if (!ne) { + ne = document.getElementById(slideIDs[0]); + snum = 0; + } + if (step < 0) {incpos = incrementals[snum].length} else {incpos = 0;} + if (incrementals[snum].length > 0 && incpos == 0) { + for (var i = 0; i < incrementals[snum].length; i++) { + if (hasClass(incrementals[snum][i], 'current')) + incpos = i + 1; + else + addClass(incrementals[snum][i], 'incremental'); + } + } + if (incrementals[snum].length > 0 && incpos > 0) + addClass(incrementals[snum][incpos - 1], 'current'); + ce.style.visibility = 'hidden'; + ne.style.visibility = 'visible'; + jl.selectedIndex = snum; + currentSlide(); + number = 0; +} + +function goTo(target) { + if (target >= smax || target == snum) return; + go(target - snum); +} + +function subgo(step) { + if (step > 0) { + removeClass(incrementals[snum][incpos - 1],'current'); + removeClass(incrementals[snum][incpos], 'incremental'); + addClass(incrementals[snum][incpos],'current'); + incpos++; + } else { + incpos--; + removeClass(incrementals[snum][incpos],'current'); + addClass(incrementals[snum][incpos], 'incremental'); + addClass(incrementals[snum][incpos - 1],'current'); + } +} + +function toggle() { + var slideColl = GetElementsWithClassName('*','slide'); + var slides = document.getElementById('slideProj'); + var outline = document.getElementById('outlineStyle'); + if (!slides.disabled) { + slides.disabled = true; + outline.disabled = false; + s5mode = false; + fontSize('1em'); + for (var n = 0; n < smax; n++) { + var slide = slideColl[n]; + slide.style.visibility = 'visible'; + } + } else { + slides.disabled = false; + outline.disabled = true; + s5mode = true; + fontScale(); + for (var n = 0; n < smax; n++) { + var slide = slideColl[n]; + slide.style.visibility = 'hidden'; + } + slideColl[snum].style.visibility = 'visible'; + } +} + +function showHide(action) { + var obj = GetElementsWithClassName('*','hideme')[0]; + switch (action) { + case 's': obj.style.visibility = 'visible'; break; + case 'h': obj.style.visibility = 'hidden'; break; + case 'k': + if (obj.style.visibility != 'visible') { + obj.style.visibility = 'visible'; + } else { + obj.style.visibility = 'hidden'; + } + break; + } +} + +// 'keys' code adapted from MozPoint (http://mozpoint.mozdev.org/) +function keys(key) { + if (!key) { + key = event; + key.which = key.keyCode; + } + if (key.which == 84) { + toggle(); + return; + } + if (s5mode) { + switch (key.which) { + case 10: // return + case 13: // enter + if (window.event && isParentOrSelf(window.event.srcElement, 'controls')) return; + if (key.target && isParentOrSelf(key.target, 'controls')) return; + if(number != undef) { + goTo(number); + break; + } + case 32: // spacebar + case 34: // page down + case 39: // rightkey + case 40: // downkey + if(number != undef) { + go(number); + } else if (!incrementals[snum] || incpos >= incrementals[snum].length) { + go(1); + } else { + subgo(1); + } + break; + case 33: // page up + case 37: // leftkey + case 38: // upkey + if(number != undef) { + go(-1 * number); + } else if (!incrementals[snum] || incpos <= 0) { + go(-1); + } else { + subgo(-1); + } + break; + case 36: // home + goTo(0); + break; + case 35: // end + goTo(smax-1); + break; + case 67: // c + showHide('k'); + break; + } + if (key.which < 48 || key.which > 57) { + number = undef; + } else { + if (window.event && isParentOrSelf(window.event.srcElement, 'controls')) return; + if (key.target && isParentOrSelf(key.target, 'controls')) return; + number = (((number != undef) ? number : 0) * 10) + (key.which - 48); + } + } + return false; +} + +function clicker(e) { + number = undef; + var target; + if (window.event) { + target = window.event.srcElement; + e = window.event; + } else target = e.target; + if (target.href != null || hasValue(target.rel, 'external') || isParentOrSelf(target, 'controls') || isParentOrSelf(target,'embed') || isParentOrSelf(target, 'object')) return true; + if (!e.which || e.which == 1) { + if (!incrementals[snum] || incpos >= incrementals[snum].length) { + go(1); + } else { + subgo(1); + } + } +} + +function findSlide(hash) { + var target = document.getElementById(hash); + if (target) { + for (var i = 0; i < slideIDs.length; i++) { + if (target.id == slideIDs[i]) return i; + } + } + return null; +} + +function slideJump() { + if (window.location.hash == null || window.location.hash == '') { + currentSlide(); + return; + } + if (window.location.hash == null) return; + var dest = null; + dest = findSlide(window.location.hash.slice(1)); + if (dest == null) { + dest = 0; + } + go(dest - snum); +} + +function fixLinks() { + var thisUri = window.location.href; + thisUri = thisUri.slice(0, thisUri.length - window.location.hash.length); + var aelements = document.getElementsByTagName('A'); + for (var i = 0; i < aelements.length; i++) { + var a = aelements[i].href; + var slideID = a.match('\#.+'); + if ((slideID) && (slideID[0].slice(0,1) == '#')) { + var dest = findSlide(slideID[0].slice(1)); + if (dest != null) { + if (aelements[i].addEventListener) { + aelements[i].addEventListener("click", new Function("e", + "if (document.getElementById('slideProj').disabled) return;" + + "go("+dest+" - snum); " + + "if (e.preventDefault) e.preventDefault();"), true); + } else if (aelements[i].attachEvent) { + aelements[i].attachEvent("onclick", new Function("", + "if (document.getElementById('slideProj').disabled) return;" + + "go("+dest+" - snum); " + + "event.returnValue = false;")); + } + } + } + } +} + +function externalLinks() { + if (!document.getElementsByTagName) return; + var anchors = document.getElementsByTagName('a'); + for (var i=0; i' + + '