User:Ilya: Difference between revisions
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===Ideas=== | ===Ideas=== | ||
*[http://meta.wikimedia.org/wiki/MediaWiki_2.0 MediaWiki 2.0] | |||
*[[OpenWetWare: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" | *[[OpenWetWare: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" | ||
*[[OpenWetWare:Software|Software]] - flexible science databases, etc | *[[OpenWetWare:Software|Software]] - flexible science databases, etc |
Revision as of 11:04, 14 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
Current
Semantic Web Ontology for the Registry of Standard Biological Parts.
Previous
Mating pheromone response pathway analysis across yeast and related species
Software
BioBricks aligner - aligns sequence reads (fragments) to Biobrick sequence
- Sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene
- A computer program for aligning a cDNA sequence with a genomic DNA sequence (backup link)
- Bio::Tools::Run::Alignment::Sim4 - wrapper for Sim4 program that allows for alignment of cdna to genomic sequences
- Bio::SearchIO::sim4 - parser for Sim4 alignments
- Bio::Tools::Sim4::Exon - a single exon determined by an alignment
- Bio::Tools::Sim4::Results - results of one Sim4 run
- Sim4.pm - CVS log (latest version)
Biology
Synthetic Biology
- Synth Bio FAQ
- DNA Hack - The website for Amateur Genetic Engineering
Misc
using analog circuits/logic in synth bio
- digital design is modular and predictable (abstraction hierarchy)
- Reshma's thoughts
- 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
Press
OpenWetWare
- Cool bio and engineering-related news
- OpenWetWare:Infrastructure
- Wikimania 2006: Boston, August 2006.
- 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
- Editing tools, including html2wiki converter based on HTML::WikiConverter Perl module
- Bulk image uploads, Perl script
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
- OpenSourceCMS - demos
- The CMS Matrix - CMS comparisons
- a list of CMS
- 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
- PLoS ONE uses TOPAZ application framework
- TYPO3
- Mambo Server
- MamboForge
- Apache Lenya- Java/XML
- Textpattern
- Magnolia
- Metadot - portal server and intranet
Development
Structure
Quality
Wikipedia Founder Sees Serious Quality Problems
Ideas
- MediaWiki 2.0
- 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
- Discussion forums
- 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
- Videntity is an OpenID registrar
Semantics
- Semantic Wiki - Wikipedia article
- SemWiki - The Semantic Wiki Community
- Category:Wikidata
- Del.icio.us-style Tags for MediaWiki
- WikiOnt is an an ontology to model that aims at integrating MediaWiki-based sites into the Semantic Web framework and making them machine-processable and -understandable
- RDF interface to MediaWiki
- RDF metadata
- DublinCoreForWiki - a suggested implementation for providing DublinCore metadata in WikiEngines.
- A sample implementation of RDF extension is in production at Wikitravel:
- RDF
- RDF Expedition
- Semantic MediaWiki
- Ontoworld - wiki for semantic web community, also a demo of the Semantic MediaWiki extension
- Wikipedia and the Semantic Web - The Missing Links - Wikimania 2005 paper
- Wikipedia and the Semantic Web - Part II - Wikimania 2006 presentation
- 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 - a list of existing Semantic Wiki Prototypes
- 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
- WikitionaryZ - a universal dictionary and thesaurus that can be queried by machines and humans.
- Flexible Fields for MediaWiki
- Live demo 1, live demo 2 and live demo 3
- Built in Types
- Wikipedia³ is a conversion of the English Wikipedia into RDF.
- Semantic Wiki features used for WWW2006 conference: Creating semantic data and Using semantic data in queries.
- RDF-compatible WikiModel
- Other implementations:
- WikSAR
- 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.
- Rx4RDF is a set of technologies designed to make W3C's RDF more accessible and easier to use. Rhizome is a general purpose content management and delivery system that runs on Raccoon. It is dynamic and self-editable like a Wiki but uses ZML and RxML to enable structured content and editable metadata.
- BettaMeta - allows users to specify the available metadata in an easy to use form
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
Wiki database
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
- WikiSpeller - spellcheck extension
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
- 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."
- 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
- Biocomicals emerged from integrating science and fun.
Science wikis
Wiki Sci is an attempt for researchers to organize research efforts in a task-oriented manner, facilitating much better idea exchange.
- Wikispecies is meant to become an open, free directory of species.
- Biocrawler
- Flu Wiki
- BioWiki
- QED wiki, aka TigerWeb; data analysis and calendar extensions
- MicrobeWiki is a free wiki resource on microbes and microbiology, edited by students at Kenyon College
- EvolvingCode.net - information about all aspects of the evolution of the genetic code
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
- Wikia - 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
- 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
- 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.
- JSON Wikipedia article
- Introducing JSON
- Web services + JSON
- YAML is a data serialization and lightweight markup language that takes concepts from languages such as XML, C, Python, and Perl.
AJAX
- Very Dynamic Web Interfaces
- 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
- AJAX Whiteboard - free minibook
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
- 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