User:Ilya

Research

Current: Semantic Web Ontology for the Registry of Standard Biological Parts.

Mating pheromone response pathway analysis across yeast and related species.

OpenWetWare

• Cool bio-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"
• Journal impact factor is a measure of importance of scientific journals. Something like this could be used to measure the success of the OpenWetWare?
• Starting to use wikicalc

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

Firefox

• Biobar
• LSID
• bioFOX

MySQL

• Java/MySQL on Linux
• Using XML with MySQL
• TurboDbAdmin - A single-page solution for exploring and editing databases from a browser.

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

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

XMLHTTP

• 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
• SAJAX: Simple Ajax Toolkit
• Dojo
• AJAX-Considered-Harmful
• Fixing AJAX
• SACK: Simple AJAX Code Kit
• Ajax Patterns
• Web Applications 1.0
• AHAH: Asychronous HTML and HTTP

Applications

• Meebo: Web 2.0 IM client
• Early AJAX Office Apps
• Bindows: desktop web applications framework
• Office 2.0 applications