User:Ilya

Research

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

Mating pheromone response pathway analysis across yeast and related species.

Bioinformatics

• DNA seen through the eyes of a coder
• Kimball's Biology Pages

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
  • Starting to use wikicalc
  • iRows

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
  • SMWRelations
  • Relation
  • Attribute
  • Category:Attribute
  • Category:Datatype
  • Semantic Wiki Use Cases
• Semantic Wiki
• 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.

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

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.
• 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

• The XMLHttpRequest object: W3C Working Draft
• 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
• SAJAX: Simple Ajax Toolkit
• Google AJAXSLT is an implementation of XSL-T in JavaScript
• 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
• Live Clipboard
• gotAPI - AJAX-based documentation resource for HTML, PHP, MySQL, Perl, Ruby, etc.

Knowledge Management

• gnowsis the Semantic Desktop environment
• Text Mining
  • Machine readability - Nature article
  • BioText - infrastructure to support the development and deployment of statistical approaches to natural language processing, which will identify entities and relations between them in bioscience texts
  • OpenText Mining Interface (OTMI)
  • Arrowsmith explores the causes of disease
  • EBIMed is a web application that combines Information Retrieval and Extraction from Medline
  • BIONLP - natural language processing of biology text] - Bob Futrelle's page
• Artificial Intelligence: A Modern Approach - this book describes the nature of knowledge, its representation, inference based on knowledge, and many other topics (sample chapters available online)