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Scratchpad update, 26 February 2010

  • The Scratchpad project is celebrating the International Year of Biodiversity by highlighting a different Scratchpad taxon page every week on our home page. This will show the breadth of taxa pages available and various methods of showing species pages.
  • A flexible way of extending taxonomy term metadata has been developed.
  • The registration page for training courses has been updated with the courses we offer in 2010 and is open for registrations.

Scratchpad update, 12 February 2010

  • On 5th February we had one of our Scratchpad team meetings. We went through the list of requests and issues raised during our Scratchpad survey last year. One request raised by many participants was the need to make the Scratchpads easier and more intuitive to use. So we are now trying to improve the workflow and the help. You might have noticed that the taskguide has changed to reflect the actual workflow better, and there are more changes coming.
  • In connection with the current year of biodiversity we also decided to put a 'species of the week' on the frontpage of scratchpads.eu. These 'species of the week' will be species pages from various Scratchpads containing actual content. In due course you will receive an email asking you to participate with your species pages.
  • On the 8th February, Vince Smith, Dave Roberts and Simon Rycroft went to Brussels for a hearing on the ViBRANT proposal, which is a big EU grant to continue and extend our Scratchpad work. We are proud to have reached this stage of the evaluation process and hope our proposal will be successful.
  • On 11-12th February we held a meeting at the NHM on how to publish articles containing new species descriptions from the Scratchpads in ZooKeys. The meeting included discussion of the workflow, the XML document needed, the content of the first paper thus produced, and a short training session for the contributors involved.
  • The manual for the basic training course was adapted so that we now have another manual for contributors and editors of Scratchpads, which they can work through on their own.

Scratchpad update, 29 January 2010

The manual for the advanced training course is now available at http://scratchpads.eu/scratchpad-training-files for everyone who wants to try on his own. It is particularly useful if you want to learn how to create views and if you want to learn how to prepare a project in secret and later publish all the data related to this project in one go. The latter uses the organic groups module and Simon has been fixing several issues with this module which became apparent during the writing of the manual.

Simon has been working on the taxonomy module and has dealt with the following:

  • Forum
  • Autotag of previously added content
  • Organic Groups Forums added
  • Advanced options hidden on the node/add or node/%nid/edit pages
  • Improved sorting of views in widgets.

I have made a start at publishing online-only publications using faunistic 'papers' on the Milichiidae and Carnidae of Greece. These publications don't include nomenclatural acts and they would never get into an impact factor journal, so it is much better to publish them online. The review process can be done by adding comments and revising the content based on these comments. In contrast to paper publications, online publications can be updated continually, but a version of the original 'copy' is still available and can be viewed by users who are logged in. By preparing these publications I have created much improved and more data rich species pages for the included species and with each further publication data will accumulate and these species pages will get better.

Scratchpad update, 15 January 2010

Simon fixed several bugs and added some new features, like having the date and time a citation of a taxon page was created showing on the page. He also worked on the auto-tagging of content.
I have been working on the manual for the training courses. The courses are now separated into a basic and an advanced course. The basic course covers basic features, administration, adding data, and taxon pages. The advanced course covers the import and management of data, organic groups, and the creation of custom content types and views.
The manual for the basic training course is available at http://scratchpads.eu/scratchpad-training-files for everyone who wants to try on his own. Please let me know if there are any problems.
Vladimir wondered whether it is possible to compare images of different species. This is actually possible by creating a new view. To check this out go to http://milichiidae.info/compare?tid_op=or&tid=Milichiella+arcuata%2C+Mil.... Try replacing the keyword with 'terminalia' or adding 'Milichiella sumptuosa'.

Regular Scratchpad updates

For the new year I have every intention of keeping up a two-weekly blog to keep you informed about what the Scratchpad team has been up to, like new Scratchpad features, bug fixes, training courses, etc.

At the beginning of December we had a Scratchpad meeting dealing with the list of bugs and feature requests. We decided that Simon would concentrate first on fixing all the "little" issues which take up to two days as well as working on the taxonomy module. As of today (6.Jan.2010), 18 issues have been fixed, for example the citation button which wasn't working on upgraded sites, and the upgrade of this website to Drupal 6. We also now have a list of all Scratchpads including some statistics on the number of users, nodes and views, which you can access at the bottom of each site under "Other Scratchpads". The "bigger" issues, mainly feature requests, have been voted on by the team and will be dealt with in order of importance.

On the 17th December we held a Scratchpad training course for 16 people at the EDIT general meeting in Caveiro (Portugal). It is always a challenge to make the course useful for experienced Scratchpad users as well as complete novices but we hope that everybody was able learn something new.

Instructions for importing a bibliography into scratchpad using the RIS-format

Written by Stephan Imhof

 

For those of us who do not use Endnote as the software for reference management, Scratchpads offer three more data formats for importing bibliographic data. For me, the RIS-format turned out to be the less complicated. Many bibliographic software has features to facilitate the export of content via this format.

 

Scratchpads paper: BMC Bioinformatics

BMC BioinformaticsAt long last we (the Scratchpad team) have got around to publishing a formal paper on the Scratchpads. There are several short notes and conference proceedings published about the work we have been doing, but this is the first technical paper that describes in details the overall architecture of the project and sets out the sociological model of what we are trying to achieve. The paper will appear as one of nine papers selected for a special series sponsored by the Encyclopedia of Life project, for the journal BMC Bioinformatics. BMC, with the help of the special issue editor Neil Sarkar, selected the Scratchpad paper to highlight the publication in a press release entitled "Darwin meets Facebook". You can find a copy of the press release attached to the bottom of this page.

Unfortunately our paper is already slightly out of date! Written in April in the run up to the eBiosphere 09 meeting, the text describes the technical architecture then, rather than now. Drupal (the underlying content management system that provides the backbone architecture) has moved on since April 09, as have many of the contributed modules we use in the Scratchpads, and the 25+ modules we have written as part of the project. Nevertheless, the paper provides the best description to date of what we are doing, and (to some extent) where we are going with this project.

The citation is:

Vincent S Smith, Simon D Rycroft, Kehan T Harman, Ben Scott and David Roberts. 2009. Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life. BMC Bioinformatics 2009, 10(Suppl 14):S6doi:10.1186/1471-2105-10-S14-S6.

The paper will be published on or around November 10th 2009, and the press release will be available here from Nov. 6th. Press queries should go through Claire Gilby, Senior Press Officer, Natural History Museum in the first instance. Tel: 020 7942 5106. Email: c.gilby@nhm.ac.uk.

Live examples for Scratchpad features

If you want to see examples of how a Scratchpad or certain Scratchpad features can look like, have a look at the websites listed below.

Scratchpad websites

Scratchpads focused on a taxonomic group

Scratchpads focused on a society or group

Scratchpads focused on a person

Scratchpad features

Bibliography

Blog

Character project

Custom content types

Distribution map

Forum

Interesting format of front page

Glossary

Groups

Images

Phylogenetic tree

Profile

Species descriptions

Species pages

Specimens

Videos

Webform

FAQ updated to Drupal 6

All FAQs have been updated and now explain how the Scratchpads work after the upgrade to Dupal 6. If your site is still on Drupal 5 you should contact the site administrator (Simon Rycroft) and ask for the upgrade.

If you have any questions or suggestions concerning the FAQs, please contact Irina Brake.

New feature: Extended content menu

With the Drupal 6 upgrade the content menu has been extended. Hovering with the mouse over a menu item will make two icons appear to the right, one for adding and one for importing data. If you click just click on the menu item you can view all nodes of this content type.

Content Menu

Written by I. Brake