OpenWetWare - OpenWetWare:Software

OpenWetWare:Software/Extensions/Analytics/GoogleAnalytics

Sat, 01 Mar 2008 23:51:36 GMT

Note: This extension is now turned on. The extension is not present in the DefaultExtensions.php file. It it only loaded for the OpenWetWare.org domain.

If anyone using a private wiki wants to get their own Google Analytics number, follow the directions below. The code must be placed in the /wikis//WikiSettings.php file at the bottom.

MANUAL ON MEDIAWIKI EXTENSIONS [1]
LIST OF MEDIAWIKI EXTENSIONS [2]

Error creating thumbnail: convert: unrecognized color `linearGradient3310) rgb(0, 0, 0'.
convert: unable to open image `linearGradient3310) rgb(0, 0, 0': No such file or directory.
convert: Non-conforming drawing primitive definition `fill'.

Google Analytics

Release status: stable

IMPLEMENTATION [3]
User activity [4]

DESCRIPTION [5]
Automatically inserts Google Analytics tracking code at the bottom of MediaWiki pages

AUTHOR(S) [6]
Tim Laqua

LAST VERSION [7]
1.2 (08-26-2007)

MEDIAWIKI [8]
1.10+

LICENSE [9]
No license specified

DOWNLOAD [10]
MediaWiki SVN [11]

EXAMPLE [12]
www.PoxWiki.com [13]

This extension inserts GOOGLE ANALYTICS tracking code in every MediaWiki page that is viewed. The extension excludes pages being view

OpenWetWare:Software/Projects/Lab Notebooks/Activity

Sat, 28 Jul 2012 00:24:23 GMT

FEATURED LAB NOTEBOOKS

* HEATHER ETCHEVERS

* The original functional genomics of human neural crest cell project [1]
* Cross-talk between neural crest and mesoderm and how the heart forms [2]
* Genetics of human eye morphogenesis [3]

* DILEEP D. MONIE

* BBF Technical Standards Promoter Measurement Test [4]

* JASON E. STAJICH

* Fungal Comparative genomics [5]

* MAURICIO BEDOYA

* Microrheology properties of Hyaluronan [6]

ACTIVITY OVERVIEW

LEGEND:
[7] = Contacted
[[image

OpenWetWare:Software

Mon, 04 May 2009 19:42:55 GMT

[1] [2]
BACK TO COMMUNITY PORTAL [3]

[4] Welcome to the OpenWetWare Software discussion area.

CONTENTS

* 1 How You Can Help [5]
* 2 Software Development [6]

* 3 Current Projects [7]

* 3.1 Editor Toolbar Extensions [8]
* 3.2 Lab Notebooks [9]

HOW YOU CAN HELP

This page links to some of the discussions ongoing about the software of OpenWetWare - please help out!
No need to be a programmer, comments are always appreciated.

SOFTWARE DEVELOPMENT

* Suggest [10] a feature!

* Report [11] a Bug!

* See [12] what we're working on this month...

* Think [13] with others about what what we can be doing better.

CURRENT PROJECTS

EDITOR TOOLBAR EXTENSIONS

* Editor Toolbar Extension Framework [14]

LAB NOTEBOOKS

* Lab notebooks [15]

* Lab notebooks overview [16]
* [[OpenWetWare:Software/P

OpenWetWare:Software/Projects/Lab Notebooks/Template Definitions

Mon, 04 Feb 2008 15:37:49 GMT

LAB NOTEBOOK TEMPLATES

COMMENTS

The following is a table of the contents of all OWW Lab Notebook templates. Documentation for all of these items will be provided.

TEMPLATES

%DPL-1.7.4-WARNING: No results!

OpenWetWare:Software/Flexible Science Databases

Sat, 23 Sep 2006 19:39:48 GMT

[1] [2]
BACK TO COMMUNITY PORTAL [3]

OVERVIEW

There is a need for a flexible database system in the sciences. Databases exist, but how many of us want to learn the messy SQL syntax, or put more than 20 records in an unwieldy Excel spreadsheet? We all have needs for a really simple way to create a database, the way that makes sense to us for our projects, not the way that is shaped by a specific tool, originally built for another purpose. We would also like really simple ways to enter that data. Those two features combined would enable all
of the scratching in the lab notebooks and envelopes to be put together digitally - indexing, searching, sharing, extending - they all become trivial.

This page is a brainstorming forum for how to shape such a tool - what it should be able to do, how to make it, what it could be used for, etc. The first major hurdle in building a tool is to come up with a concrete concept - the hope is that we ca

OpenWetWare:Software/Network Protocols/Bonjour

Mon, 01 Sep 2008 21:54:17 GMT

Bonjour (software) 241896 151257341 2007-08-14T21:39:52Z Tomasf 1479354 /* Overview */

Bonjour
Image:Apple Bonjour Logo.png [1]

DEVELOPER(S) [2]
Apple Computer [3]

STABLE RELEASE [4]
107.6 / 2006-09-18 [5]

OPERATING SYSTEM [6]
Mac OS X [7], Windows [8], GNU/Linux [9]

TYPE [10]
Zeroconf [11]

LICENSE [12]
Apache License [13] 2.0

WEBSITE [14]
http://developer.apple.com/bonjour [15]

BONJOUR, formerly RENDEZVOUS, is Apple Inc. [16]'s trade name [17] for its implementation of Zeroconf [18], a service discovery [19] protocol used in Apple's Mac OS X [20] operating system [21] f

OpenWetWare:Software/Extensions

Wed, 08 Jun 2011 21:15:30 GMT

[1] [2]
BACK TO COMMUNITY PORTAL [3]

INSTALLED EXTENSIONS

Go to Special:Version [4] to see the definitive list of installed extensions and their versions. See OpenWetWare:Feature test [5] to check that the extensions are working. If you wish to discuss extensions on openwetware, sign up for the mailing list [6].

The following extensions are installed on OpenWetware:

CRITICAL EXTENSIONS

Critical extensions are either those which if they break would cause many pages to "break" and as such, these extensions should be considered as important to support (for upgrades, etc). Another way to look at this: if we aren't willing to support these, then we shouldn't encourage people to use these. The known dependencies of these are listed to help in smooth upgrades.

* BIBLIO [7]: for citing from PubMed. (Requires php w/ builtin curl support)
* [[OPENWETWARE:SOFTWARE/EXTENSIONS/

OpenWetWare:Software/Online Database Access/GenBank Accession Numbers

Mon, 15 Nov 2010 02:26:16 GMT

GenBank Accession Numbers

ACCESSION

The unique identifier for a sequence record. An accession number applies to the complete record and is usually a combination of a letter(s) and numbers, such as a single letter followed by five digits (e.g., U12345) or two letters followed by six digits (e.g., AF123456). Some accessions might be longer, depending on the type of sequence record.

Accession numbers do not change, even if information in the record is changed at the author's request. Sometimes, however, an original accession number might become secondary to a newer accession number, if the authors make a new submission that combines previous sequences, or if for some reason a new submission supercedes an earlier record.

Records from the RefSeq database of reference sequences have a different accession number format that begins with two letters followed by an underscore bar and six or more digits, for example:

* NT_123456 constructed genomic contigs
* NM_123456 mRNAs
* NP_123456

OpenWetWare:Software/Extensions/Biblio

Tue, 04 May 2010 10:50:26 GMT

DESCRIPTION

The BIBLIO extension for MediaWiki written by Martin Jambon [1] allows users to define and cite bibliographic entries by their key. It also downloads bibliographic references from PubMed and formats them using only the PubMed identifier (PMID). Similarly, books can be cited using their ISBN. OpenWetWare is currently using version 0.7.

HOW TO USE

You can easily add citations by typing Goldbeter-PNAS-1981 Jacob-JMB-1961 Ptashne-Genetic-Switch Website which gives [1 [2], 2 [3], 3 [4], 4 [5]].

To insert a list of references type

#Goldbeter-PNAS-1981 pmid=6947258
#Jacob-JMB-1961 pmid=13718526
// you can even leave a comment on a paper
#Ptashne-Genetic-Switch isbn=0879697164
#Website http://openwetw

OpenWetWare:Software/Extensions/ParserFunctions

Sun, 18 Nov 2007 06:54:51 GMT

OpenWetWare:Software/Exensions/ParserFunctions

A collection of parser functions [1] such as branching instructions and expression handler and time calculation unit.

Template:H:h [2]

Shortcut [3]:
[[WM:PF [4]]]

OTHER LANGUAGES: Template:ParserFunctions [5]
The Template:Wpd [6] extension PARSERFUNCTIONS is a collection of parser functions [7] (note the difference between the name of the collection, and the general term). These parser functions have a hash character in front of the function name, so they typically have the syntax: Template:Ft [8]

FUNCTIONS

Tip: _With Special:ExpandTemplates [9] one can evaluate expressions with parser functions directly._

This module defines eight functions at present: expr [10], if [11], ifeq [12], ifexist [13]

OpenWetWare:Software/Extensions/Renameuser

Sun, 18 Nov 2007 06:55:35 GMT

SOFTWARE/EXTENSIONS/RENAMEUSERS

from http://www.mediawiki.org/w/index.php?title=Extension:Renameuser">

Error creating thumbnail: convert: unrecognized color `linearGradient3310) rgb(0, 0, 0'.
convert: unable to open image `linearGradient3310) rgb(0, 0, 0': No such file or directory.
convert: Non-conforming drawing primitive definition `fill'.

Renameuser

Release status: stable

Image:SpecialRenameuser.png [4]

IMPLEMENTATION [5]
User identity [6],Special page [7]

DESCRIPTION [8]
Special page allows user accounts to be renamed

AUTHOR(S) [9]
Ævar Arnfjörð Bjarmason [10]

MEDIAWIKI [11]
1.7.0+

LICENSE [12]
No license specified

DOWNLOAD [13]
from Subversion [14]
CHANGELOG [15]

ADDED RIGHTS [16]

renameuser

RENAMEUSER provides a special page which allows authorised users to rename user accounts. This will cause page histories, etc. to be updated.

REQUIREMENTS

This extension requires MediaWiki version 1.7.0 or greater. Due to the nature of this extension, and its use in production on Wikimedia web sites, it is often updated, and can become incompatible wit

OpenWetWare:Software/Extensions/MultiUpload

Sat, 17 Nov 2007 22:50:34 GMT

MANUAL ON MEDIAWIKI EXTENSIONS [1]
LIST OF MEDIAWIKI EXTENSIONS [2]

Error creating thumbnail: convert: unrecognized color `linearGradient3310) rgb(0, 0, 0'.
convert: unable to open image `linearGradient3310) rgb(0, 0, 0': No such file or directory.
convert: Non-conforming drawing primitive definition `fill'.

MultiUpload

Release status: stable

Image:MultiUpload Screenshot.png [3]

IMPLEMENTATION [4]
Special page [5]

DESCRIPTION [6]
Allows users to upload more than 1 file at time.

AUTHOR(S) [7]
Travis Derouin [8]

LAST VERSION [9]
0.1 (2007-01-19)

MEDIAWIKI [10]
1.6+

LICENSE [11]
No license specified

DOWNLOAD [12]
via SVN [13]

PARAMETERS [14]

$wgMaxUploadFiles

The MULTIUPLOAD extension allows users to upload more than one file at a time, it tries to reuse as much functionality in Special:Upload as possible.

WARNING: This extension does not work with Mediawiki 1.11+, due to some significant changes to SpecialUpload.php. A fix for this is forthcoming.

LICENSE

Copyright 2006 Travis Derouin, wikiHow

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This pr

OpenWetWare:Software/Extensions/Calendar

Sat, 17 Nov 2007 21:50:30 GMT

SOFTWARE/EXTENSIONS/CALENDAR

Copied from: http://www.mediawiki.org/wiki/Extension:Calendar_%28Cdamian%29 [1]

MANUAL ON MEDIAWIKI EXTENSIONS [2]
LIST OF MEDIAWIKI EXTENSIONS [3]

Error creating thumbnail: convert: unrecognized color `linearGradient3310) rgb(0, 0, 0'.
convert: unable to open image `linearGradient3310) rgb(0, 0, 0': No such file or directory.
convert: Non-conforming drawing primitive definition `fill'.

Calendar (Cdamian)

Release status: beta

IMPLEMENTATION [4]
Tag [5]

DESCRIPTION [6]
Use tags to create a calendar

AUTHOR(S) [7]
Cdamian [8]Talk [9]

LAST VERSION [10]
1.13

MEDIAWIKI [11]
1.6.0 - 1.11.0

LICENSE [12]
No license specified

DOWNLOAD [13]
http://krass.com/software/ [14]

A few people have asked me for the calendar I use on krass.com

I couldn't release it earlier, because the CalendarClass I used didn't have a GPL friendly license (in fact, it didn't have any license and I wasn't able to contact the author). Now I have written my own primitive class and can release the whole thing under GPL.

It's just tested on http://krass.com/ [15] and not tested in any other environment. PLEASE USE HTTP://KRASS.COM/WIKI/SANDBOX/CALENDAR [16] FOR TESTING. NOT THE MAIN ONE!

You can find the code here: http://krass.com/software/ [17]

USERS

* [ht

OpenWetWare:Software/Extensions/UserMerge

Sun, 18 Nov 2007 21:10:48 GMT

MANUAL ON MEDIAWIKI EXTENSIONS [1]
LIST OF MEDIAWIKI EXTENSIONS [2]

Error creating thumbnail: convert: unrecognized color `linearGradient3310) rgb(0, 0, 0'.
convert: unable to open image `linearGradient3310) rgb(0, 0, 0': No such file or directory.
convert: Non-conforming drawing primitive definition `fill'.

User Merge and Delete

Release status: stable

IMPLEMENTATION [3]
Special page [4],User identity [5]

DESCRIPTION [6]
Merges references from one user to another user in the Wiki database - will also delete old users following merge

AUTHOR(S) [7]
Tim Laqua

LAST VERSION [8]
1.0 (07-27-2007)

MEDIAWIKI [9]
1.10+

LICENSE [10]
No license specified

DOWNLOAD [11]
MediaWiki SVN [12]

USER MERGE AND DELETE extension allows Wiki users with the 'userrights' permission (Bureaucrat by default) to merge one Wiki user's account with another Wiki user's account - deleting following merge is also supported. You may not delete a user without merging first - omitting the "New User" field will auto-populate the New User as User ID 1 (Usually WikiSysop) and ask you to confirm merge to Admin. Merging to Anonymous (ID0) is not supported.

INSTALLATION

* Create a new

OpenWetWare:Software/My Links/New Member List

Sat, 09 May 2009 21:13:57 GMT

* Labs
* Courses
* Protocols
* Materials
* Resources
* FAQ
* Help:Starting a lab wiki
* Help:Notebook/One Click Setup

OpenWetWare:Software/Projects/Editor/Toolbar

Mon, 04 May 2009 21:30:57 GMT

Adding the formula editor to OWW would be great. To get it to work, I've first inserted a new set of pages to OWW that implement a set of extension to the standard editor that will be pretty useful by themselves. There's a much-needed simple table form that will be a blessing in addition to providing the basis for the formula editor.

This is a Javascript extension. It's not globally enabled it yet. However, it's in place and working for anyone who wants to test it.

To add it, edit the link below with your "User_Name" and open it:

[[User:User_Name/monobook.js]]

Once you have the link open in your editor, insert the following expression:

document.write('

OpenWetWare:Software/Projects/Chat/Transcripts

Wed, 26 Nov 2008 14:17:20 GMT

* 14/02/2008 17:57:06 ‹Mackenzie L. Cowell› great
* 14/02/2008 17:57:32 ‹Bill Flanagan› it will save me a lot of time if there's one I can just plug into.
* 14/02/2008 17:58:48 ‹Mackenzie L. Cowell› We should look at the model the http://www.opencoffeeclub.org/ [1] uses - they may already have some good ideas / infrastructure
* 14/02/2008 17:59:04 ‹Lorrie LeJeune› Another possibility is for the coffee session or meetup to be hosted in a different location each month.
* 14/02/2008 17:59:08 ‹Bill Flanagan› get bck to me if anyone finds one.
* 14/02/2008 18:00:20 ‹John Cumbers› I have to go, I'll start a discussion on the list about how this went and maybe we should try and set some guidelines as to how to get the most out of these int he future
* 14/02/2008 18:00:29 ‹John Cumbers› and when to have the next one
* 14/02/2008 18:00:48 ‹John Cumbers› we didn't get onto the discussion about publishing req.
* 14/02/2008 18:00:59 ‹John Cumbers› but we have a teleconf. at

OpenWetWare:Software/Extensions/Dewikify

Sat, 17 Nov 2007 15:54:37 GMT

See the OpenWetWare:Dewikify/Demo [1] page for the dewikify process in action.

OWW DEWIKIFYING

To take advantage of the dewikify script on OpenWetWare, all your pages must be under one namespace [2]. For the following, let's suppose you're using the Foo namespace. Then you can access the dewikified version of http://www.openwetware.org/wiki/Foo [3] as http://foo.openwetware.org/ [4]. All links from this page to other pages that begin with Foo: (like http://www.openwetware.org/wiki/Foo:Bar [5]) will be dewikified. Other pages will not be dewikified. Dewikifying happens automatically as
long as the above namespace convention is met.

The conversion is done simply by capitalizing the first letter, e.g. foo to Foo on the wiki. However, if your namespace has a different capitalization, spaces, punctuation, or you just wish to have an alias, then you will need to contact us to do a mapping for you, e.g. syntheticbiology is mapped to Synthetic_Biology.

PAGE TEMPLATE

OpenWetWare:Software/Feature requests

Mon, 13 Oct 2008 16:29:27 GMT

Please add feature requests/comments to this page. The list is prioritized by the Steering committee [1]. The most important features are implemented by the senior tech developer. See this page [2] for the features currently being implemented.

INFORMATION CONTRIBUTION

TOP PRIORITIES

* Publish to OpenWetWare button for private wiki\'s and external wiki\'s [3]
* Seeding of user pages upon account creation [4]
* Auto-generation of lab notebooks [5]

FULL LIST

_Tools that encourage contribution of new content / improve existing content_

* Hooks for Genbank, SwissProt etc.

* Initially, this might be just an extension to Biblio to allow referencing by accession number. Eventually, this could pull in info from databases.
* See also http://blogs.nature.com/wp/nascent/2007/07/scientific_blogging_plugins.html [6]

* Protocols

OpenWetWare:Software/Analytics/Alexa

Fri, 03 Oct 2008 20:06:51 GMT

OpenWetWare:Software/Performance/Squid

Thu, 04 Sep 2008 19:49:48 GMT

WHY SQUID?

Squid [1] is a high-performance proxy server that can also be used as a HTTP accelerator for the webserver. Explained in layman terms, Squid will store a copy of the pages served by webserver and the next time the same page is requested, Squid will serve the copy. This process is called "caching" and it removes the need for the webserver to regenerate that same page again, resulting in a tremendous performance boost for the webserver.

Since MediaWiki websites are generated dynamically entirely, there is a substantial performance gain [2] in running Squid as a HTTP accelerator for your webserver. In fact, sites like Wikipedia use several Squid caches to enhance their performance.

Because of this performance gain, MediaWiki has been designed to integrate closely with Squid. For example, MediaWiki will notify Squid when a page should be purged from the cache in order to be regenerated.

THE ARCHITECTURE

OpenWetWare:Software/Server/Apache

Fri, 22 Aug 2008 01:16:10 GMT

Log Rotation [1]

OpenWetWare:Software/Server/Apache/Log Rotation

Fri, 22 Aug 2008 01:18:08 GMT

LOG ROTATION

On even a moderately busy server, the quantity of information stored in the log files is very large. The access log file typically grows 1 MB or more per 10,000 requests. It will consequently be necessary to periodically rotate the log files by moving or deleting the existing logs. This cannot be done while the server is running, because Apache will continue writing to the old log file as long as it holds the file open. Instead, the server must be restarted after the log files are moved or
deleted so that it will open new log files.

By using a graceful restart, the server can be instructed to open new log files without losing any existing or pending connections from clients. However, in order to accomplish this, the server must continue to write to the old log files while it finishes serving old requests. It is therefore necessary to wait for some time after the restart before doing any processing on the log files. A typical scenario that simply rotates the logs and

OpenWetWare:Software/Server

Fri, 22 Aug 2008 01:12:51 GMT

OWW SERVER-RELATED SOFTWARE

* Virtual Machines [1]
* Apache [2]

OpenWetWare:Software/Server/Urchin/Log Rotation

Fri, 22 Aug 2008 01:11:02 GMT

LOG ROTATION BEST PRACTICES

From Google Support [1]

OVERVIEW

It is very typical in most operating environments for the system services and applications such as webservers to generate logfiles that record actions and events related to those services. In most cases, it is also standard practice for the operating system and/or applications to perform regular maintenance on the logfiles to keep the size of the logfiles in check. This prevents the logfiles from growing without bounds and eventually running out of disk space.

A common approach to managing logs is to have a regularly scheduled log rotation task that renames the existing logs with a timestamp and then restarts the service or application with a new, zero length logfile. It is also a standard practice for the log rotation task to compress the old logfiles, and to delete logfiles after a certain age or rotation cycle threshold has been reached.

I

OpenWetWare:Software/Server/Urchin/Log Rotation/WebLogRotate

Fri, 22 Aug 2008 01:09:53 GMT

* !/usr/bin/perl -w
*
* RCS ID: $Revision: 1.7 $
*
* Script to rotate the specified logs and name them with yesterday's
* date. The script also restarts the web server with a specified command.
* and optionally compresses old logs and removes them after a certain period.
*
* Copyright (c) 2002, 2003, 2004 Urchin Software Corporation
*
* Usage: weblog_rotate.pl [--log /path/to/log [--log /path/to/log]
* | [--loglist /path/to/loglist]]
* --touchlog
* --restart_cmd "apachectl restart"
* --compress --days N --help
*
* Where:
* --loglist specifies the path to a file containing the full pathnames
* of all the logs that are to be rotated. This option cannot be used
* with the --log option.
* --log specifies the full path to the log file to be rotated
* (multiple --log entries are allowed)
* --touchlog specifies that a new log should be created once the
*

OpenWetWare:Software/Server/Urchin

Fri, 22 Aug 2008 01:04:09 GMT

Urchin Log Rotation [1]

OpenWetWare:Software1

Tue, 05 Aug 2008 13:52:12 GMT

OpenWetWare:Software/My OWW Links

Fri, 25 Jul 2008 23:55:23 GMT

CONTENTS

* 1 Page Link Management in OWW [1]

* 1.1 Bill Flanagan: OpenWetWare.org [2]
* 1.2 "Links Page" [3]
* 1.3 "Links Page" Sections [4]

PAGE LINK MANAGEMENT IN OWW

BILL FLANAGAN: OPENWETWARE.ORG

The purpose of this development task is to create a facility within OWW to allow logged-in OWW members to save references to OWW pages on a personal "links" page or set of pages.

"LINKS PAGE"

The "links page" will be limited to storing links to and from OWW pages. A feature of this page will allow an OWW member to not only see their own links but those of any other OWW member.

"LINKS PAGE" SECTIONS

On the page, all links will initially appear as individual line items on a single page. Users will be able to divide the page into sections. Each section will have a name. Nomenclature is important here. These section headings may play the same role as "categories". However, since the term "category" has a very specific definition within MediaWiki systems, these section header titles should not be confused with OWW category names.

Section names assigned within the "links page" will not be exported to

OpenWetWare:Software/Projects/Search/Google/Custom Search/Removing Ads

Mon, 14 Jul 2008 21:51:06 GMT

Link: [1] [1]

You have two opportunities to disable ads on your Custom Search Engine. You can select the Do not show ads option when you first create a Custom Search Engine, or you can follow the steps below to disable advertising on your existing Custom Search Engine:

* Click the My search engines link on the left-hand side of the Overview page.
* Click the control panel link next to the name of your search engine.
* Under the Preferences section of the Control panel page, select the Advertising status option that reads 'Do not show ads on results pages (for non-profits, universities, and government agencies only).'
* Click the Save Changes button.

Engine:

http://www.google.com/coop/cse?cx=008120968908463339035:bio9cgvtfz4 [2]