Dear Stefan,

The academics in Nutritional Biochemistry who are involved with teaching and using various aspects of bioinformatics are myself, Dr Tim Parr and Dr Rob Bardsley. If you would like to come down and talk to us about your project and how we might be able to help, I'm sure that can be arranged. Cheers, John Brameld

************************************

Message 2

Cc’d to tim parr, Ronald bardsley

Dear John

Further to your previous email, I have now written a brief introduction to the areas of research in which myGrid is involved, which I've attached to this email.

I've been asked to investigate how people using bioinformaticians perform bioinformatics tasks. This information will be used to validate ideas produced by myGrid so far, and to feed into future design work. This could include details such as what databases and other applications you use, how data is stored (both temporarily whilst a task is being performed, and for persistence), and the potential for automation of the tasks which you perform. It would probably be good to record any discussion I have with you so that I can transcribe it. I would like to collect, if possible, examples (such as spreadsheets, data etc) of how people do computing, and ideally we would like to collect enough to be able to reconstruct a particular bioinformatics task in our lab.

If you're still interested and willing to help, I appreciate it very much! If so, would it be possible to arrange an initial meeting to plan how to gather some of the information that we're interested in, and also so that I can get some ideas of papers I can read etc to find out more about what ares of work you are involved in. I'm currently free on any day up to (and including) 24th December, but a meeting either earlier in the day (eg 9-10ish) or later in the day (eg 5-6ish) would be great, as I live in Loughborough so the Sutton Bonington campus would either be on my way to work or on the way home. I am, however, completely flexible and happy to meet when it suits you best.

Cheers!

Stefan

********************************************************************

Message 3: from John Brameld

Hi Stefan, Sorry I didn't reply before xmas, but things were a bit hectic here. If you can make it, I've sorted out for myself, Tim Parr and Ron Bardsley to be available for a meeting around 9:15am on Thursday 15th January, here at SB (North Lab). We have a meeting room which includes a computer projector if you want to use it. It would probably be better for you to explain what you are after and we can then hopefully help (and maybe you can help us as well). Let me know if that's OK and if you need directions. My office is North lab, 1st floor, room no. 43.

Cheers,

John

********************

Message 4 (after having been asked where the Human Genome Mapping Project website was

Hi Stefan,

The URL is:
http://www.hgmp.mrc.ac.uk/

Cheers, John

********************

Message 5

Dear John

A few people in Nottingham are interested in having a look at the 3rd year bioinformatics practical that you gave me a copy of, so I was wondering if it would be acceptable for me to scan my copy of it and place it on our project website, or if you would prefer me not to?

I'm going to get started on a demo of Taverna using the work in this practical, so hopefully soon I'll be able to come over and show it to you.

Cheers Stefan

****************

Message 6

Dear John

I've now finished demos of workflows in Taverna for sections 1-3 of the 3rd year bioinformatics practical that you gave me, and if you were still interested in seeing them, then I'll come over and show you.

To run the demos, I'll need a machine with Java installed onto which I can copy some software. If you don't have any machines with java installed, then I can just copy it across too, so there shouldn't be any problem - admin rights are not needed for any of this. The machine has to be able to access the internet, and I'll need to know the address and port number of any web proxy that is used (eg on my machines, these are wwwcache.cs.nott.ac.uk and 3128).

Cheers Stef

********************

Message 7

forgot to say that the machine should be a pc running windows.

Stef

******************

Message 8

Dear Stef, Sorry it has taken so long to get back to you, but we've all been up to our necks with teaching, exams and research. Now the students have finished we have some time and would very much like to see a demo of what you've done. I've spoken to Ron and Tim and the 25th June (Friday - at anytime) would be a good day for all of us (Tim and Ron have a conference next week and I have one on the monday and tuesday of the following week). Is this OK for you? If not let me know some alternatives and I'll co-ordinate with Tim and Ron.

Cheers,

John

*****************

Message 9

Yes, should have mentioned that. The workflows access web services at places like the EBI, so at networked computer is necessary. If you are set up to access the web through a web proxy, I'll need to know details of settings for this -eg for me, here in the department of computer science are

proxy host = wwwcache.cs.nott.ac.uk (ie the computer on which the proxy is running) proxy port = 3128 (port to connect to on this computer)

You may be able to find these out by looking at your web browser, which has to be set up to use a proxy if it is required.

eg on internet explorer, go to the tools menu, select internet options, click the connections tab, click LAN settings. I then get a box asking for either an automatic configuration script, or for the proxy host and port. If a configuration script is specifed, email me the URL and I can extract deatils of your proxy from this configuration script, or if a proxy host and port are specified you can send me these.

Stef

******************

Message 10

Hi Stef,

A configuration script is specified at http://wwwcache.nottingham.ac.uk/proxy.pac

See you friday 25th Cheers, John

************

Message 11

To run Taverna as installed on your machine, open a DOS window, and type

cd c:\stefan

and then type runme3

That should be it!

If you want to move it to another machine, I'd copy the entire contents of directory c:\stefan over. You then might have to edit runme3.bat on your new machine so that it know where java is. There's a line in the file which says something like

set path=c:\program files\java\j2sdk1.4.2\bin;%path%

You just need to modify that to point to the right place. Let me know if you have any problems.

Taverna is being updated fairly regularly as people suggest improvements and bug fixes, so a new release seems to be made available every few months. Releases are downloaded from the Taverna website, http://taverna.sourceforge.net. There is a users mailing list, details of which are on the mailing list - you'll find out about new releases here, and the people developing Taverna watch this, so any requests you make for changes are likely to be picked up fairly quickly. It isn't a high-volume mailing list - I get about 5 emails a week I reckon. If you do decide to download a new release, you'll need to set it up for your web proxy settings as i did. Luckily, the directory of Taverna releases doesn't seem to change any more, so you'll be able to use runme3.bat without modification. So to get a new release working, download its zip, unzip this to a directory (eg c:\release11) and then copy runme3.bat into c:\release11. Run this batch file in the same way as before, and things should work.

The best way to get into Taverna (and it isn't difficult) is to follow Peter Li's tutorial - he's a biologist working at Newcastle and mostly building simple workflows for common tasks. Go to http://taverna.sourceforge.net and click Tutorials, then click "Dr Peter Li's Taverna Tutorial".

The Taverna web pages are also useful to get lists of available web services to use in Taverna. Click "What service are available?" Another source is the mygrid web pages - have a look at

http://twiki.mygrid.org.uk/twiki/bin/view/Bioinformatics/BioinformaticsWebServices

though this list is often the same as Taverna web page. Web services are begining to get more popular as a way of providing asccess to services, so if you currently use an html based service, it's worth having a look to see if an equivalenet web service exists.

I've passed on the suggestion that was made on Friday about loading lists of values from files rather than having to add them individually to the input panel to Taverna's developers, and they're going to start working today on doing this. So soon you 'll probably be able to specify a file containgin a comma-seperated list of values into an input. Taverna deals with lists of values in an interesting way - eg if you provide a list of accession numbers to an input, and if the next step was to look up a sequence for an accession number, the output of that step created by Taverna would then be a list of sequences (Taverna does the iteration automatically). I've realised that this mechanism could be used to produce a workflow which used clustalw to align an arbitray number of sequences, rather than having to write workflows with 1,2,3 etc inputs. All Taverna needs is the facility to turn a list of strings (eg strings containing sequences) into one string which is the concatentation of all the strings in the list. This could then be passed to the clustalw web service which was in the demonstration I showed you. I've requested this feature be added to Taverna, and I think that has been done already! So, hopefully soon I'll be able to send you a workflow which could be used to load a list of accession numbers from a file, get their sequences, and then align these sequences against each other.

Tim suggested the task of using a protein name to look up all proteins whose name matched, looking up their nucleotide sequences and aligning them against each other. I'm interested in building a workflow to do this - I think this hasn't been done yet by other people in myGrid. I was wondering if you or he could send me a brief description of how you would look up the proteins and get their sequences currently using web pages. I'll then have a look around for web services to do the same task, and send you the workflow when I get it working.

Anyway, thanks for your time on Friday. The information you've provided has been really useful. Any questions about Taverna, and any suggestions for useful workflows to build, would be very welcome.

Stef

*************

Message 12

I forgot to ask you if you could email me runme3.bat. I want to keep a record of what proxy settings have worked for different people in the university, so that when I do more demos I shouldn't have the same problems as I did on Friday!

Stef

************

Message 13

Hi Stef

Attached is the runme3.bat file. I'm afraid everyone's going or gone on holiday, so may take some time to reply to your previous message with regards to pulling out proteins/genes from different species. We tend to simply search for the name of the gene/protein we're interested in. For example Tim works on calpains and calpastatin and therefore would search the DNA or protein databases for those terms. My group work on growth hormone (GH) and insulin like growth factors (IGF) and their receptors so would search for those terms, but in they are also known as somatotropin and somatomedin as well. Hope this helps - Tim should be in touch in the near future as well.

Cheers,John

***********

Dear John

When we first me, you mentioned the bioinformatics resources at http://www.hgmp.mrc.ac.uk/ that you use, including stuff like NIX, PIX etc. I've got myself an account here and been doing some experiments. However, I've noticed that these resources are going to be closed as of roughly next July. I was wondering if there were any other similar collections of tools that you were planning to move to using as a replacement. I'm interested in knowing so that I can go and look that these too!

Cheers,Stefan