User:Ilya

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Graduate student in Bioinformatics at Northeastern University working in Endy Lab at MIT.

Contact: [math]\displaystyle{ \mbox{ilyas} }[/math]@[math]\displaystyle{ \mbox{mit.edu} }[/math]

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

OpenWetWare

  • Slashdot article: History Flow shows how wiki articles evolve.
  • Semapedia - connecting virtual and physical worlds
  • Wiki Science is the study of how the phenomenon of wikis, and free, open collaborative works in general (like free software and open source), are growing, changing and adapting.
  • WikiMatrix - wiki software comparison

Wiki Markup

Science wikis

Wiki Sci is an attempt for researchers to organize research efforts in a task-oriented manner, facilitating much better idea exchange.

Wikis in education

  • Wikis in Education - proceedings of Wikimania 2006
  • Wikiacademia - a web application which manages course wikis with a markup syntax and feel similar to MediaWiki but with the addition of assignments, grades, and access rights.

Development

Parser Functions

Structure

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

Searching

Misc

Resources

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

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

Miscellaneous

  • Biotool2Web: Creating Simple Web Interfaces for Bioinformatics Applications
  • Sedna is an open source XML-native database management system developed from scratch in C/C++ and Scheme

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 (JavaScript Object Notation) 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.

Life Sciences

  • Nature on blogging in science
  • 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.
  • SIPHS is a peer support network for researchers in the biological and biomedical sciences
  • iHOP - a gene network for navigating the literature

XMLHTTP

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
  • Unobtrusive Javascript
  • Helma project - Javascript application framework
  • Mochikit - a lightweight Javascript library
  • Sarissa

XML Data Islands

XML Data Islands @ AjaxPatterns

Applications

  • reddit - what's new online
  • Wufoo - making forms easy
  • Meebo: Web 2.0 IM client
  • 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
  • Terminal

Mashups

  • Frappr - create your own custom map
  • gotAPI - AJAX-based documentation resource for HTML, PHP, MySQL, Perl, Ruby, etc.

Office

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