- Do not be afraid. (I used to be afraid, but there is no need). Nobody has ever made me feel unwanted (there have been robust discussions, but none angry). So I go to WP and search for “Open Data”. (The capitalisation may be important – always start with a capital if you can). There is no such page, but it offers one a start
So by clicking on the first link you get a fresh page headed “Open DataNo page with that title exists.
You can create this page or request it.
2. You don’t have to write the whole page at once. Even the title and a few words is enough. This is a “stub” and others can add to it or modify it. Let’s see how far we get before nightfall. 3. Read some WP pages to get a sense of style. Good ones have an introductory paragraph and then the body, made of several labelled sections. Then there are usually links to other WP pages, and finally references. WP is very insistent on good references. Of course you don’t have to have them all at once. 4. You can always backtrack if you get something wrong. WP saves everything. No-one minds if there are 100 versions of something. Indeed if you are on a flaky connection you may wish to make a number of small changes and save after each. 5. You don’t have to let people know who you are. I do, but I don’t expect it from others. You can use an IP or (if registered) an alias, or a real name. I use “petermr” which is not difficult to crack (use Google). If you are registered then add a signature (~~~~ is the magic) which links to your own WP Talk page.Since all the edits are recorded, I can simply link to them!
- Page creation. Note that WP has formatted the page nicely (I simply have to remember that there is no need for a title, that each section has ==foo== and to add {{stub}} at the bottom. The links go in [[..]], e.g. [[Open Access]]. I’ve saved it after a paragraph as it’s dinner time. Any visitor will see that it’s a new page (stub) – they may or may not feel they want to add something. It’s not my page, it’s our page. However it’s probably good manners to wait a day or so before editing a new page.
- Here is the history of the edits. Notice that a Wikipedian has already spotted the article and removed the “stub” before me!
- Here is the latest version. It’s not “mine” – it’s ours. Anyone can edit it – I am sure at least there are typos and many other links and references can be added.
- the real final version tonight.
As you can see some of the files are green and some are orange. The orange ones are those I have changed since “last time”. Last time of what? last time I used the
This cheerful fellow (developed initially by
(The pink ones are new). Since there were one or two serverside changes I now have to re-test the system (the changes might break my code). In this case the test passes. Sometimes it requires a lot of work to merge the changes – that’s normally a good thing because someone else is working with you. Now let’s re-update in case the server has changed. No? Did I create any new files? I check with “Add contents” – yes, I did. (This is where I most frequently goof up – unless I send these files to the server my collaborators won’t see them. And their systems will then fail). So I add the files, and then “Commit”.
Now everyone in the project can update from my latest changes…
Some of you will have thought “what happens if two people make changes to the same file at the same time?” CVS will try to merge the changes. If they are in different parts of the file it’s probably OK. If not there will be a conflict. This is a bit of a pain, and normally involves reverting to the older version and then agreeing between the two people what changes each wanted to make and why. In many projects – such as CDK – the active developers keep a chat room open so they can send messages like “I need to change X – does anyone mind?” Much better than technical mechanisms.
Here’s the final commit:
CVS is now being superseded by
oh dear! it’s brown. I’ll just @Ignore that one test and…
and it’s GREEN!
(But I haven’t fooled anyone. The @Ignore is just lying in wait to bite me in the future…) 

============ OR ===========
===== the compound information looks like ========
Note that compounds are identified by a bold identifier ( e.g. 38) which normally increases in serial order throughout the text. This is fragile, in that the insertion of a new number requires manual editing throughout the text (this is confirmed by various chemical gurus). Compounds are drawn in the middle of free text sections, and again in the compound information. There are no tools to enforce consistency between the numbering and the diagrams. Moreover information such as reagents, yields, physical and analytical data are repeated in several places. These have to be manually transcribed and (unless you tell me differently) this is a tedious, frustrating and error-prone process.
Moreover at this stage of writing the thesis the student has to assemble all the data for the 200 compounds. Are they all there? Could any of the spectra be muddled? Is that figure in the lab book a 2 or a 7? Heaven help if a spectrum is missing and the compound has now decomposed into a brown oil or got lost in the great laboratory flood. Of course none of this ever happens…
So are you all happy with how you authored or will author your thesis? I haven’t even touched on how peaks are transcribed from spectra and how the rigmarole of spectra peaks has to be authored and formatted. If so, I’ll shut up. Else I will make some serious and positive suggestions in a later blog.