More about journal clubs

This is to alert people to the fact that there is an online journal club meeting on 13th March at 8pm UK time. You can find more information here: http://infolitjournalclub.blogspot.co.uk/2013/02/online-journal-club-13-march-ancil.html I will be talking more about this on the researchers' meeting in the iSchool on 14th March.

Also if people want something to read about reading clubs, what they are and why people use them, a useful paper is:
Deenadayalan, Y, K Grimmer-Somers, M Prior, and S Kumar. (2008) “How to run an effective journal club: a systematic review.” Journal of evaluation in clinical practice, 14 (5), 898-911.

Vivas and other scary things

At the last researchers' discussion, a request was made for reports from the frontline - i.e. - could people who have just had a viva tell others for whom it is still a future hurdle, what sort of questions they were asked and what sort difficulties they encountered.

James Wallace (who contributed to this blog recently) had just successfully passed his upgrade viva (congratulations!) and made the following points:

"People need to be made aware that the whole point of the exercise is that the examiner is wanting to find ways of proving how good you are, rather than trying to cause problems. It's not a case of trick questions - if something is asked that seems straightforward, it probably is, although no-one will object if you take a little time to think things through. 

"In my case, the questions were based on discussion points from my own text, so making sure you familiarise yourself with your work before the day is a good idea."

Following the session however, we decided to try putting the following questions to students who have just completed their viva.  Hopefully they'll yield some interesting answers.

1. What is the title of your thesis?
2. Can you provide an abstract (for inclusion in this blog)?
3. How did you prepare for your viva?
4. How long did your viva take?
5. Is there anything you wish you had done differently?
6. Did the examiners concentrate on any particular section of your thesis?  If so, which?
7. Can you describe any part of your viva where you were pleased with your performance?
8. What was it you did that pleased you?
9. Can you describe any part of your viva where you were dissatisfied with your performance?
10. What was it you did that dissatisfied you?
11. Please give an example of a question that you found hard.
12. Why was it hard?
13. What was the outcome of your viva?
14. Please give some examples of the sort of corrections you need to make (if any).
15. Were they classed as minor or major?
16. Do you have any tips for looking and feeling confident in front of the examiners?
17. Can you think of any good advice that you would give to students who are preparing for their viva?

Blogging for research

In yesterday's researchers' session, I led a discussion about blogging for research. I gave a bit of background about my interest in blogging, which I first talked about in one of these sessions almost two years ago (see my original post here). I also talked briefly about a session discussing blogging at the University of Pittsburgh last November - my blogpost describing that session is available here.

Yesterday's discussion covered a range of useful topics including:

• How blog use by researchers may differ depending on their disciplinary perspectives - for example, issues surrounding commercially sensitive information which are a particular consideration in chemoinformatics projects, or the more detailed, reflective approach to methodology development which is such a significant part of the social science research process.
• How other social media tools - such as Twitter and Facebook - can be used to engage with potential research participants - and may themselves form the basis for research studies.
• The range of audiences which a blogger may be writing for (people I know, people I'd like my research to help) and the actual audience which a blog might reach (potentially a global audience and including people who are willing to engage in the discussion and to comment, question and criticise).
• The tension between all the things which a researcher could potentially post about, and those things which the individual researcher feels comfortable discussing in such a public forum. This may be further complicated by ethical considerations, or issues relating to prior publication.
• Using blogs such as this one (and these discussion sessions) to engage in a more collaborative and open way to address common problems encountered by researchers, by exploring practical questions such as "what survey tool should I use?"
• Using the blog (and the discussion sessions) to provide an opportunity for people further along in the PhD process to reflect back on their experiences. In particular, the viva experience was identified as something which could potentially be demystified by future discussions / posts.

In the course of the discussion about this final point, I mentioned a really helpful discussion led by Liz Brewster back in February 2011 - "Things I wish I'd known before I started my PhD" - this is the link to the post.

I was also asked about the most popular post on my own blog. At the time, I couldn't recall which this was but, having checked the statistics, this post about PG Cafe Forum from May 2011 is at the top of the list. At the time PG Cafe Forum didn't have it's own website, and it seems that my blog entry was one of a relatively small number of Google-able sources with these words in the title - it seems that by giving the post that title, I was engaging in some unintentional search engine optimisation!

Blog-post journal club

At the researchers' discussion yesterday (where the discussion topic was blogging), I briefly mentioned that I am co-organising a new online journal club for information literacy, that has had two blog-post discussions so far. The blog is here: http://infolitjournalclub.blogspot.co.uk/
I have also co-hosted a journal club in Second Life for a couple of years: this shows some snippets of the first meeting in 2010.





I will be talking about journal clubs in one of the future researcher discussions. Marshall Dozier (my SL Journal Club co-organiser) and I are doing some research into the club, and have done a literature search. A good starting point is:

Deenadayalan, Y. et al (2008) How to run an effective journal club: a systematic review. Journal of Evaluation in Clinical Practice, 14 (5), 898-911.

Information Retrieval (but not as we know it)

Last month, James Wallace bravely volunteered to lead a discussion based on his project work.  In so doing, he proved the title of this post to be wrong.

He is the second member of the chemoinformatics group to post on this blog (after Ben Allen) and he did an excellent job of helping the rest of us to understand the kind of work the group does.

There are occasional signs of bemusement amongst members of the iSchool about the position of chemoinformatics.  It is not always obvious how its work relates to that of others in the school who deal with the organisation of libraries, and the management of information in businesses.  But James began his talk with a few words that fitted chemoinformatics firmly at the heart of the iSchool: words such as 'classification', 'organisation', 'information retrieval' and 'database'.

It quickly became clear that he was using tools with which we were all familiar, but applying them to a subject that most of didn't understand (the classification of molecular structures).  What was interesting though, was the extent to which the nature of information retrieval (IR) he was discussing seemed historical.  Anyone involved with IR pre-Google would have found themselves on familiar territory.  One of the questions raised was whether or not a Google-type approach would be relevant to chemoinformatics.  The feeling was that it probably wouldn't - in part because it may be necessary to have a critical mass of users before a system such as PageRank could be useful.  I don't know whether or not that's true, but if it is, it would be interesting to know what the critical mass might be, and what factors would cause it to vary.

"Using network and graph theory to influence drug design" (by J.E.A. Wallace)

Chemoinformatics (also known as ‘cheminformatics’) applies computational and information science techniques to a range of chemical problems.  These techniques are used, for example, to model compounds and to predict their properties.  Chemoinformatics has made it possible to simulate expensive operations such as high-throughput screening (the rapid testing of numerous compounds for desirable qualities).  A good starting point for those new to the field is the book ‘An Introduction to Chemoinformatics’ by Leach and Gillet.

My project is specifically concerned with the idea of de novo design (Latin for ‘from new’).  De novo design builds novel molecules in virtual space and evaluates them against some measure of functionality, such as similarity to a compound known to work well, or the complementarity between the shape of the molecule and the receptor it is to fill. The aim is to streamline the drug discovery process.  By referring to these virtual compounds, it may be possible to reduce the number of synthesis operations necessary. However, the sheer number of potential molecules that can be made renders it impossible to explore all of chemical space for solutions, even with modern levels of computing power. As a result, various predictive sampling processes (such as the Monte Carlo method) have been adapted for use in this field. These can give good results, but their simplistic approach to constructing molecules can lead to products being generated that are impossible to fabricate in real world situations, limiting the overall usefulness of the methods.

In order to work around such problems, methods have been developed within the chemoinformatics group that use genuine reaction data from literature to create generic rules (the reaction vectors).  These rules can be applied to a given starting material to generate new molecules. This provides a compromise between finding novel molecules and retaining a synthetic awareness, as each transformation is based on a literature precedent. However, this method has its own limitations.  Some structures for example, can be built up using multistep reaction sequences. In many cases, the intermediate steps in such sequences do not resemble either the end product or the starting material in terms of similarity to the target.  Consequently, many potentially useful molecules are never completed because steps en route to the end product score poorly.

One solution to this problem is to create a new rule format that represents all the reaction steps in one operation. This requires some initial identification of those sequences, which is where my project comes in. If we regard a chemical reaction as a transformation of one molecule into another, it becomes possible to connect these transformations together into a network.  Every path through the network will represent a multistep synthetic route for which each step has a known example in the literature.  Reaction properties such as ease of synthesis, cost of materials, yield of product etc. can then be added to the network to bias the selection of routes in accordance with a particular set of criteria.

Libraries and Information Society research group meeting

This is another post about a recent meeting of the Libraries and Information Society research group (last Wednesday). Angharad Roberts talked about her visit to the University of Pittsburgh iSchool, USA (which she also blogged about in the last post here). She explained some of the differences in structure and approach of the PhD programmes in Pittsburgh and at Sheffield (for example, there is a much larger taught element in the Pittsburgh programme) and we discussed a few of the pros and cons of each. As part of her visit Angharad had participated in a session about academic writing. One of the texts for this was:
Sword, H. (2012). Stylish academic writing. Harvard University Press.
This led on to an interesting discussion about our own experience of academic writing and in particular our use of the first person ("I"): when we felt we could use it and what the alternatives were. We also talked a little about journal editor's expectations and our experiences in submitting articles.
The next meeting of the whole group (staff and research students) is on 12th December at 3.30pm.