User:Ilya
From OpenWetWare
Research
Current: Semantic Web Ontology for the Registry of Standard Biological Parts.
Mating pheromone response pathway analysis across yeast and related species.
Bioinformatics
Synthetic Biology
using analog circuits/logic in synth bio
- digital design is modular and predictable (abstraction hierarchy)
- Reshma's thoughts
- Synth Bio FAQ
- Analog Logic: Continuous-Time Analog Circuits for Statistical Signal Processing by Ben Vigoda
- Analog circuit Wikipedia article
- Research in analog IC design
- Circuit simulator applet
- Analog design resources
- Basic Analog Circuits - Tutorial
OpenWetWare
- Cool bio and engineering-related news
- Wikimania 2006: Boston, August 2006
- Editing tools, including html2wiki converter based on HTML::WikiConverter Perl module
- Slashdot article: History Flow shows how wiki articles evolve.
Ideas
- Ideas discussion area - "the goal is some flexible framework where it is easy to create and modify databases on the fly, with nice user interfaces for database entry"
- Software - flexible science databases, etc
- Journal impact factor is a measure of importance of scientific journals. Something like this could be used to measure the success of the OpenWetWare?
- online spreadsheet
Semantics
- Del.icio.us-style Tags for MediaWiki
- RDF interface to MediaWiki
- A sample implementation of RDF extension is in production at Wikitravel:
- RDF
- RDF Expedition
- Semantic MediaWiki
- Specialpages
- SearchTriple
- Special:Categories: a complete list of all categories
- Special:Relations: a complete list of all relations; Category:Relation is deprecated
- Special:Attributes: a complete list of all attributes (not just the ones with articles); Category:Attribute is deprecated
- Special:Types: a complete list of all datatypes; Category:Datatype is deprecated
- Semantic Wiki Use Cases
- Inline queries
- Semantic Wiki State Of The Art
- Knowledge structure (from Semantics page @ ontoworld.org)
- Categories are a means to classify articles according to certain criteria. For example, by adding [[Category:City]] to an article, the page is tagged as describing a city.
- Relations can be viewed as "categories for links". An article on Berlin contains a link to "Germany" that has a special meaning: it was put there since Berlin is the capital of Germany. To make this knowledge available to computer programs, one would like to "tag" the link. This is done by writing [[is capital of::Germany]].
- Attribute: a special type of relations/categories: [[population:=3,396,990]]
- Datatypes: the prefix "Type:" is again a separate namespace that distinguishes descriptive articles about types from normal pages: [[has type::Type:integer]] to say that the special relation "has type" holds between Attribute:population and Type:integer.
- Semantic templates can be used to support the consistent usage of annotations
- Semantic Wiki - a Wikipedia article
- Flexible Fields for MediaWiki
- Live demo 1, live demo 2 and live demo 3
- Platypus Wiki - a Semantic Wiki WikiWeb. It uses RDF (Resource Description Framework), RDF Schema and OWL (Web Ontology Language) to create ontologies and manage metadata.
- Built in Types
- Wikipedia³ is a conversion of the English Wikipedia into RDF.
- Semantic Wiki used for WWW2006 conference
- RDF-compatible WikiModel
Searching
- LuMriX Wikipedia Search - dynamic search in style of Google Suggest
- WikiWax - your quick index to Wikipedia (based on LookAhead by SurfWax)
- Suggestion - Ajax Patterns
Misc
- Google Analytics
- blacklist certain pages from public viewing and/or editing (Blacklist pages from viewing)
- use "endy members group" to restrict access to certain pages
- Biblio.php - citation module
Resources
- Siphs - a peer enabled search engine and online reference for the life sciences research community.
- MetaCollab - a collaboration on collaboration.
- Declan Butler, Nature on blogging in science
- Wikinomics - an open documentation initiative in the field of bioinformatics and systems biology.
- Biology Wiki
- Nodalpoint - a bioinformatics weblog.
- taqdot - news for the open source and synthetic biology community.
Software
Eclipse
- Eclipse Web Tools Platform (WTP):
- source editors for HTML, Javascript, CSS, JSP, SQL, XML, DTD, XSD, and WSDL
- graphical editors for XSD and WSDL
- J2EE project natures, builders, and models and a J2EE navigator
- a Web service wizard and explorer, and WS-I Test Tools
- database access and query tools and models
- Bioclipse - an integrated biochemistry workbench
- Java Development Tools (JDT) subproject
Firefox
MySQL
- Java/MySQL on Linux
- Using XML with MySQL
- TurboDbAdmin - A single-page solution for exploring and editing databases from a browser.
- Using MySQL with Java
LIMS
- CERF Notebook by Rescentris Ltd
- Capture and share files, notes, data - your entire research record
- 21CFR11 compliant - role-based access, digital signatures, audit trails, and more
- Extensible - Customizable - integrate with existing solutions & databases
- Custom templates ensure uniform recordkeeping across your organization
- Windows, Mac, Linux
- eLab Notebook by Waters Corp
- NuGenesis SDMS "Information Management Platform" by Waters Corp
- STARLIMS web-based LIMS
Web 2.0
- PorgrammableWeb - directory of mashups, APIs, tagging, etc
- Web 2.0 by Paul Graham: "Web 2.0 means using the web the way it's meant to be used. The "trends" we're seeing now are simply the inherent nature of the web emerging from under the broken models that got imposed on it during the Bubble."
- What Is Web 2.0 by Tim O'Reilly
- JSON is a data interchange format that can be trivially parsed by JavaScript, with JavaScript's built in eval() procedure.
- YAML is a data serialization and lightweight markup language that takes concepts from languages such as XML, C, Python, and Perl.
- Unobtrusive Javascript
- reddit - what's new online
- Wufoo - making forms easy
Life Sciences
- Nature on blogging in science
- From Science in the web age: Science in the web age: The expanding electronic universe: "Young scientists are often reluctant to express their thoughts online out of fear that it is somehow inappropriate, or even possibly damaging to their careers."
- From Science in the web age: Joint efforts: "...younger researchers, in particular, are concerned that scientists are missing out on new ways to communicate with each other and the public."
- Biolicious - tagging for biology
- CiteULike is a free service to help academics to share, store, and organise the academic papers they are reading
- Connotea is a free website to help researchers and clinicians manage and share information.
- Postgenomic collates posts from life science blogs.
- iSpecies - the mashup returns a page with NCBI genomics information, Yahoo images of the species, and articles culled from Google Scholar.
XMLHTTP
- haXe - web oriented universal language
- Ajax news
- Two tools bring Ajax to Eclipse's Ajax Toolkit Framework: Dojo and Zimbra
- XMLHTTP is a set of APIs that can be used by JavaScript and other web browser scripting languages to transfer XML to and from a web server using HTTP.
- Ajax: A New Approach to Web Applications
- AJAX-Considered-Harmful
- Fixing AJAX
- Ajax Patterns
- AHAH: Asychronous HTML and HTTP
Specifications
- The XMLHttpRequest object: W3C Working Draft
- Web Applications 1.0 This specification introduces features to HTML and the DOM that ease the authoring of Web-based applications. Additions include the context menus, a direct-mode graphics canvas, inline popup windows, server-sent events, and more.
Software development kits
- Google Web Toolkit (GWT) is a Java software development framework that makes writing AJAX applications easy. With GWT, you can develop and debug AJAX applications in the Java language using the Java development tools of your choice. When you deploy your application to production, the GWT compiler translates your Java application to browser-compliant JavaScript and HTML.
- AJAXSLT is an implementation of XSL-T in JavaScript
- Yahoo! UI Library is a set of utilities and controls, written in JavaScript, for building richly interactive web applications using techniques such as DOM scripting, DHTML and AJAX.
- SAJAX: Simple Ajax Toolkit
- Dojo toolkit
- SACK: Simple AJAX Code Kit
- Bindows: desktop web applications framework
- Live Clipboard
Applications
- Meebo: Web 2.0 IM client
- gotAPI - AJAX-based documentation resource for HTML, PHP, MySQL, Perl, Ruby, etc.
- ajaxSketch is a web-based drawing tool that provides a familiar environment for diagramming, creating flow charts, free hand drawing and more
- Writeboard - shareable, web-based text documents
Office
- Early AJAX Office Apps
- Office 2.0 applications
- gOffice
- Word processors
- Writely (part of Google)
- Spreadsheets
- EditGrid
- Google Spreadsheets
- ajaxXLS Viewer is a web-based spreadsheet viewer that allows you to easily open any .xls file within your Firefox browser
- NumSum
- iRows
