FrontPage

BioImage Wiki

This Wiki contains shared notes relating to the Image Bioinformatics Research Group activities in the Zoology department at Oxford University. It is intended for information that is mainly internal to the working group. There is also an older wiki here.

To access the rest of this wiki, you may need to be logged in. If you are not already logged in, please do so now using the login link at the top of this page. The first time you do this, you need to create a user profile and choose a password. A cookie may be set so that on subsequent accesses the login is handled automatically. When logged in, the login name is shown at the top of the page, with UserPreferences in place of the login link.

Contents

1. Image Bioinformatics Research Group
2. Public resources and uploads
3. Data Webs
4. FlyData - Drosophila Gene Expression Laboratory Data
5. FLY-TED - Drosophila Testis Gene Expression Database
6. FlyWeb - Data Web for Linking Laboratory Image Data with Repository Publications
7. Older project information
   1. Bioimage database
   2. Others
8. Technical infrastructure
   1. General technical infrastructure notes
   2. This system (bioimage.ontonet.org)
   3. Other IBRG systems
   4. Notes from Twiki on Milos
   5. Making a snapshot of a Media Wiki
   6. BioImage internal mailing list
   7. Support links
9. How to use this site
   1. New user?
   2. Local page templates

1. Image Bioinformatics Research Group

• Personnel

• Administration

• Publications

• Presentations

• RelatedReferences - add interesting links to this page

• OtherResources: images, data, etc

• IdeasForExploration

See also:

• Research Group web site - http://ibrg.zoo.ox.ac.uk/

• ImageWeb activities - http://imageweb.zoo.ox.ac.uk/

• Ontogenesis network - http://ontogenesis.ontonet.org/moin/FrontPage

• IbrgAdministration - for general technical and administrative information about IBRG, systems, IP addresses, etc. http://bioimage.ontonet.org/moin/IbrgAdministration

• IbrgPlanning - for research group activity planning notes

• Technical notes - http://milos2.zoo.ox.ac.uk/ibrgtech/index.php

2. Public resources and uploads

• PublicResources: publicly accessible files and resources

• UploadResources: publicly accessible file upload page

3. Data Webs

• DataWebs - general notes and links relating to our data webs ideas

• DataWebsPlanning

• DefiningImageAccessPlanning

• Defining Image Access follow-on project

  • 20070803Teleconference - notes from teleconference with Balviar Notay

• DatawebsMeetings

• DatawebsRecruitment

4. FlyData - Drosophila Gene Expression Laboratory Data

Decision Support and Semantic Organization of Laboratory Data in Drosophila Gene Expression Experiments.

• FlyData data files - see DTGED

• MaxD - possible platform for FlyData: http://www.bioinf.manchester.ac.uk/microarray/maxd/

5. FLY-TED - Drosophila Testis Gene Expression Database

• DTGED - Drosophila Testis Gene Expression Database project

6. FlyWeb - Data Web for Linking Laboratory Image Data with Repository Publications

• http://imageweb.zoo.ox.ac.uk/wiki/index.php/FlyWeb_project - Project page

• [....] - Project proposal

7. Older project information

7.1. Bioimage database

• BioimageDocumentation

• BioimageInstallation (Also notes for maintaining the current BioImage installation, and Ruby/Rails/PostgreSQL instllation notes)

• BioimageOntology

• Bioimage viewcvs

• SubmissionInterface

• BioimageHandoverPlan - outline plan for handing over responsibility for Bioimage maintenance

• BioImageHandoverNotes

• ProtegeNotes - notes for using Protege

• RacerDetails - command line options for racer reasoner

7.2. Others

• OntoImage project

8. Technical infrastructure

• IbrgWebSites - Technical notes about our public web sites

• IbrgAdministration - For general technical and administrative information about IBRG, systems, IP addresses, etc. ( http://bioimage.ontonet.org/moin/IbrgAdministration)

• NetworkedResources - overview of servers and facilities provided

8.1. General technical infrastructure notes

• ScientificLinux - RedHat Enterprise Linux 4 clone aimed at scientific users.

• CentosLinux - another RedHat Enterprise Linux clone.

• VMWareNotes

• LinuxNotes

• TomcatInstallation

• DevelopmentTools (rsync+ssh notes, eclipse, stuff on svn and cvs could also go here)

• CalendarLinks

• ZakynthosSetup - Infrastructure base system setup notes

8.2. This system (bioimage.ontonet.org)

• Wiki user configuration

• OntonetServer (see also: http://antiparos.zoo.ox.ac.uk)

  • http://www.ontonet.org/moin/ServerConfiguration/WikiConfiguration - MoinMoin Wiki Configuration

  • http://www.ontonet.org/moin/ServerConfiguration/BackupUsingTsm - Server backup using Tivoli HSM/TSM

  • http://www.ontonet.org/moin/ServerConfiguration/MailManConfiguration - Mailing list and message archive software installation and configuration

  • http://www.ontonet.org/moin/ServerConfiguration/SecurityChecklist - Security checklist notes

8.3. Other IBRG systems

• http://milos2.zoo.ox.ac.uk/ibrgtech/index.php/Milos_setup - Milos

• Paros

• AntiParos

• Amorgos

• Andros

• Zakynthos

• Delos

8.4. Notes from Twiki on Milos

• http://milos2.zoo.ox.ac.uk/twiki/bin/view/Main/WebHome - original wiki

• http://milos2.zoo.ox.ac.uk/twiki/bin/view/Bioimage/WebHome - older BioImage wiki documentation pages

• http://milos2.zoo.ox.ac.uk/twiki/bin/view/Main/UsefulInfo - older admin pages

• http://milos2.zoo.ox.ac.uk/twiki/bin/view/Main/MachineIPs - list of machines and addresses

8.5. Making a snapshot of a Media Wiki

• Download and install HTTrack or WinHTTrack website copier ( http://www.httrack.com/)

• Use HTTrack to copy wiki web site to a temporary directory. Other files from the same server may also be copied, but HTTP query URIs are not dereferenced, which means the resulting snapshot still contains live edit links back to the main web site.

• Use a bulk text editor to change (or remove) absolute HTTP URI references to the original web site.

• (Optional: use bulk text editor to remove section edit links.)

8.6. BioImage internal mailing list

• Mailing list information: http://lists.ontonet.org/mailman/listinfo/bioimage

• Mailing list archives at: http://lists.ontonet.org/mailman/private/bioimage/ (member-only)

• Mailing list posting: mailto:bioimage@mail.ontonet.org

8.7. Support links

• https://wiki.oucs.ox.ac.uk/itss/SupDell - Oxford Dell supplier page

9. How to use this site

You must be logged in to edit pages on this site: if not logged in, a "Login" link is shown at the top of any page. After login, this changes to your logged in user name.

A Wiki is a collaborative site, anyone can contribute and share:

• Edit any page by pressing Edit at the top or the bottom of the page

• Create a link to another page with joined capitalized words (like WikiSandBox) or with ["quoted words in brackets"]

• Search for page titles or text within pages using the search box at the top of any page

• See HelpForBeginners to get you going, HelpContents for all help pages.

To learn more about what a WikiWikiWeb is, read about WhyWikiWorks and the WikiNature. Also, consult the WikiWikiWebFaq.

This wiki is powered by MoinMoin.

9.1. New user?

If you are new to this wiki, please perform the following steps:

• Click the login link at the top of this page

• Enter your name (using CamelCase)

• Enter a password , password confirmation and email address

• Click on the "Create profile" button

Now you should be able to view the rest of this site.

You also need a site administrator to add your login name to the list of users allowed to edit the wiki pages, which is listed at UserGroup.

9.2. Local page templates

• GeneralTemplate