User:Ilya: Difference between revisions

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*[http://ds9a.nl/amazing-dna/ DNA seen through the eyes of a coder]
*[http://ds9a.nl/amazing-dna/ DNA seen through the eyes of a coder]
*[http://biology-pages.info/ Kimball's Biology Pages]
*[http://biology-pages.info/ Kimball's Biology Pages]
===Online tools===
*[http://weblogo.berkeley.edu/logo.cgi WebLogo] - create sequence logos


==Synthetic Biology==
==Synthetic Biology==

Revision as of 10:21, 8 September 2006

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

Bioinformatics

Online tools

Synthetic Biology

Misc

using analog circuits/logic in synth bio

Press

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

Tools

Editors

CMS

  • arguments for using a content management system:
    • there is some internal info that will not benefit from being world-writeable or even -readable
  • Drupal
    • PHP, MySQL, Apache
    • easy install
    • good for communities and hobbyst projects
    • simple and clear internal structure, which requres minimum time for learning to use and administer it
    • example site: Pharmer.org
    • "all content is available as soon as it's written" model
  • Plone
    • Python, Zope (may use Apache)
    • industrial, heavy-duty CMS system
    • good for large corporate and intranet sites
    • more powerfull permissions system

Development

Parser Functions

Structure

Quality

Wikipedia Founder Sees Serious Quality Problems

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
  • OpenID

Semantics

Searching

Wiki database

Misc

Resources

  • The Synaptic Leap - Open Source Biomedical Research for the 21st Century
  • 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.
  • Nodalpoint - a bioinformatics weblog.
  • taqdot - news for the open source and synthetic biology community.
  • Synthetic Pages - is a freely available interactive database of synthetic chemistry.
  • BIOSCI/Bionet is a set of electronic communication forums - the bionet USENET newsgroups and parallel e-mail lists - promotes communication between professionals in the biological sciences
  • BioResearch Online is an online community that serves the product-sourcing and information-seeking needs of bioresearch professionals working on biopharm manufacturing, RNA, enzymatic reactions, biopharm contract manufacturing, as well as fermentation, pathogens, filtration, research and biopharm testing
  • 50 popular science blogs from 2006
  • Biohackers News for life science Nerds. Biology that matters.
  • Protocol Online - your lab's reference book
  • 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

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.

Wiki hosting

  • [http://www.wikia.com/ a collection of communities with websites that you can edit
  • PBwiki - free collaborative editing
  • ProjectForum is software that makes it easy for a team of people to work together

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

  • Biobar
  • LSID
  • bioFOX
  • MIT LibX is a toolbar that allows you to quickly search the Barton catalog, Vera, Google Scholar, the SFX FullText Finder and other search tools

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
  • Freezer management LIMS?
  • SLIMS Small Laboratory Informatics Management System is geared toward chemoinformatics and biological assays but can be extended with new datatypes
  • GnosisLIMS is a project to create a fully functional Open Source Laboratory Information Management System

Application servers

  • Whitebeam - open source; applications are written as a set of XML pages that contain embedded JavaScript

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
  • Aggregate Data utilizes AJAX-based "sliders" so survey takers can choose anywhere along a spectrum of opinion
  • CHM file viewers for non-Windows platforms

Web 2.0

  • 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.

AJAX

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
  • COWS Ajax makes cross-site, asynchronous, tri-directional communication (the user, your site, the application host) a no-brainer
  • 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
  • Lazybase - easy online databases
  • infogami lets anyone build good-looking, easily-editable web sites
  • Google Pages
  • 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

  • PorgrammableWeb - directory of mashups, APIs, tagging, etc
  • Frappr - create your own custom map
  • gotAPI - AJAX-based documentation resource for HTML, PHP, MySQL, Perl, Ruby, etc.

Office

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