The common factor with all of the designed templates was the need to edit the template at BBCode level via the “edit post” box to input data. The change in the usability of the blog came with the introduction of template automation and the implementation of the drop down menu as had been the vision in the original template design. This allowed the addition of posts to the blog containing data by directly using the template, rather than the addition of an empty template which had the data added afterwards. This coupled with the optimised data structure allowed use of the blog to increase in effectiveness.
Once created, the new templates could be used through a new form generated from the ‘use template’ button on the blog, and did not need to be edited at the BBCode level. The templates included drop down menus for selecting other blog posts, thereby allowing easy selection of the correct post to be added in each cell requiring a link.
Each procedure arranged in a row. Loss of reagent metadata term – the linked posts are generated from the metadata.
4.2.3.1 Creating the templates
In section 4.2.1.1 the basic commands used to code a table in BBCode was introduced. The new templates are still based on these basic commands, but extra commands are used to generate the added functionality. Double brackets [[ ]] are used as markers which produce editable boxes and lists when the template is viewed as a form. The double brackets also store links when the template is saved as a post. The double brackets have instructions inside them which describe the desired function. For example the command [[box]] would be used to prepare a text box that might be used for specifying the quantity of a reagent. This command would be written inside a particular cell of a table. Leaving the cell blank will produce a box that cannot be edited without using the ‘edit post’ function, whilst writing text in the cell would produce a cell containing text that cannot be edited without using the ‘edit post’ function.
In the same way that [[box]] is used to produce a box, a dropdown list is prepared using double brackets and the metadata tags. For example to produce a list of buffers the command [[Post_type:Buffer]] must be used. Post type is the metadata key and Buffer is the value of that key. For lists where one or more post types could apply for example ‘Plasmid’ and ‘plasmid (uncharacterised)’ then the command [[Post_type:plasmid%]] would be used. The % sign selects from all metadata key values containing the word plasmid. These things can all be demonstrated in the following code for a table that would produce part of a transformation template:
[table][mrow]Reaction[mcol]Cells[mcol]Quantity[mcol]Plasmid[mcol]Quant ity[mcol]Product[/mrow]
[row]1[col][[Post_type:cell_strain]][col][[box]][col][[Post_type:plasm id%]][col][[box]][col][[Post_type:strain_(uncharacterised)]][/row]...
The words reaction, cells, quantity, plasmid and product would show up in the form and would not be editable from the form. Cells given the command [[box]] would be empty and editable, whilst those given the command [[Post_type:]] would produce drop down lists.
An example of part of a template post displayed on the blog (figure 4.9) shows the commands [[box]] and [[Post_type:]], plus boxes with pre-set data/titles added. In this example compared to the code above, the term “μL” has been used rather than “quantity”. The template also demonstrates how commands in double brackets do not have to be used within a table. At the bottom of the post, [[Post_type:strain_(uncharacterised)]] is used to form the first words of a sentence of free text as the post it is linked to can also form the first words of the sentence. The command has also been formatted to allow the text to show up bold in the final displayed post. This example shows the post as it would be displayed on the blog in the news feed or through selecting templates. To access the template as a useable form, the “use template” function would be selected from the post (not shown).
Figure 4.9: part of a template for an electroporation procedure showing how the drop down box and text box functionality is prepared using [[]] and non-editable text is prepared by pre-writing in the post during template creation.
It took time to prepare and create the new templates ready for use, but the time was not considered to be a burden due to the advantages of using working templates, and the time that would be gained back for future practical research.
4.2.3.2 Posts must be named systematically to aid the use of automated
templates
When a drop down menu is selected in the form, each post in the list appears by name. If the name is ambiguous, it is much more difficult to select the correct post. This slows down research as time is consumed checking on the blog for the exact name of the required post. This problem highlighted the importance of how post titles were named and what data they contained, as the titles of the posts must provide adequate information for the correct post to be selected when using the menu. Therefore a new system for naming posts systematically to introduce a greater degree of clarity was implemented.
Pre-included text
Boxes which can have text added
Previously post names had been randomly assigned usually with the paper lab book reference being a major part of the title. This was changed to a system assigning each post an experiment number, experiment name and round number to indicate which round of the cycle the experiment belonged to. This is because there are four repeated rounds in each experiment. If the post was a repeat of a previous experimental post, an attempt number was also added. This was a matter of user choice and each individual blog user can define post titles as they choose. In this instance experiments continued to be assigned an experiment number based on the system used in the paper laboratory book, though the use of the paper book had been abandoned.
The naming convention was started just prior to starting the generation of library JH2. Therefore the course of experiments from that library is much easier to follow as will be shown later.