Cameron Neylon

Two rather exciting things are happening at the moment. Firstly we have
finally got the LaBLog system up and running at RAL
(<http://biolab.isis.rl.ac.uk>). Not a lot is happening there yet but we
are gradually working up to a full Open Notebook status, starting by
introducing people to the system bit by bit. My first experiment went up
there late last week, it isn't finished yet but I better get some of the
data analysis done as rpg, if no-one else, is interested in the results.

The other area of development is that back down in Southampton, Blog
MkIII is being specced out and design is going forward. This is being
worked on now by both Mark Borkum and Andrew Milsted. Last time I was
down in Southampton Mark asked me for some use cases -- so I thought I
might use the experiment I've just recorded to try and explain both the
good and bad points of the current system, and also my continuing belief
that anything but a very simple data model is likely to be fatally
flawed when recording an experiment. This will also hopefully mark the
beginning of more actual science content on this blog as I start to
describe some of what we are doing and why. As we get more of the record
of what we are doing onto the web we will be trying to generate a useful
resource for people looking to use our kind of facilities.

So, very briefly the point of the experiment we started last week is to
look at the use of GFP as a concentration and scattering standard in
Small Angle Scattering. Small angle x-ray and neutron scattering provide
an effective way of determining low resolution (say 5-10 A) structures
of proteins in solution. However they suffer from serious potential
artefacts that must be rigorously excluded before the data analysis can
be trusted. One of those most crucial of these is aggregation, whether
random conversion of protein into visible crud, or specific
protein-protein interactions. Either of these, along with poor
background subtraction or any one of a number of other problems can very
easily render data and the analysis that depends on it meaningless.

So what to do? Well one approach is to use a very well characterised
standard for which concentration, size, and shape are well established.
There are plenty of proteins that are well behaved, pretty cheap, and
for which the structure is known. However, as any biophysicist will tell
you, measuring protein concentration accurately and precisely is tough;
colorimetric assays are next to useless and measuring the UV absorbance
of aromatic residues is pretty insensitive, prone to interference with
other biological molecules (particularly DNA), and a lot harder to do
right than most people think.

Our approach is to look at whether GFP is a good potential standard
(specifically an eGFP engineered to prevent the tetramerisation that is
common with the natural proteins). It has a strong absoprtion, well
clear of most other biological molecules at 490 nm, it is dead easy to
produce in large quantities (in our hands, I know other people have had
trouble with this but we routinely pump out hundreds of milligrams and
currently have a little over one gramme in the freezer), is stable in
solution at high concentrations and freeze dries nicely. Sounds great!
In principle we can do our scattering, then take the same sample cells,
put them *directly in a spectrophotometer*, and measure the
concentration. Last week was about doing some initial tests on a lab
SAXS instrument to see whether the concept held up.

So -- to our use case.

Maria, a student from Southampton, met me in Bath holding samples of GFP
made up to 1, 2, 5, and 10 mg/mL in buffer. I quizzed Maria as to
exactly how the samples had been made up and then recorded that in the
LaBLog ([post
here](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/79)). I
then created the four posts representing each of the samples
([1](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/78),
[2](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/81),
[3](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/82),
[4](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/83)). I
also created [a template for doing
SAXS](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/75),
and then, using that template I started filling in the first couple of
planned samples (but I didn't actually submit the post until sometime
later).

At this point, as the buffer background was running, I realised that the
[10mg/mL
sample](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/78)
actually had visible aggregate in it. As the [5 mg/mL
sample](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/81)
didn't have any aggregate we changed the planned order of SAXS samples,
starting with the 5 mg/mL sample. At the same time, we [centrifuged the
10 mg/mL
sample](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/85),
which appeared to work quite nicely, generating a new, [cleared 10 mg/mL
sample](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/86),
and prepared [fresh 5
mg/mL](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/88)
and [fresh 2
mg/mL](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/87)
samples.

Due to a lack of confidence in how we had got the image plate into its
reader we actually ended up running the [original 5 mg/mL
sample](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/81)
three times. The second time we really did muck up the transfer but
comparisons of the first and third time made us confident the first one
was ok. At this point we were late for lunch and decided we would put
the [lowest concentration (1 mg/mL)
sample](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/83)
on for an hour and grab something to eat. Note that by this time we had
changed the expected order of samples about three or four times but none
of this is actually recorded because I didn't actually commit the record
of data collection until the end of the day.

By this stage the running of samples was humming along quite nicely. It
was time to deal with the data. The raw data comes off the instrument in
the form of an image. I haven't actually got these off the original
computer as yet because they are rather large. However they are then
immediately processed into relatively small two column data. It seems
clear that each data file requires its own identity so those were all
created (using [another
template](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/90))
. Currently, several of these do not even have the two column text data,
the big tiff files broke the system on upload, and I got fed up with
uploading the reduced data by hand into each file.

As a result of running out of time and the patience to upload multiple
files, the [description of the data
reduction](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/123)
is a bit terse, and although there are links to all the data most of you
will get a 404 if you try to follow them, so I need to bring all of that
back down and put it into the LaBLog proper where it is accessible but
if you look closely
[here](http://biolab.isis.rl.ac.uk/projects/blog/blogs.php/bit_id/123#com),
you will see I made a mistake with some of the data analysis that needs
fixing. I'm not sure I can be bothered systematically uploading all the
incorrect files. If the system were acting naturally as a file
repository and I was acting directly on those files then it would be
part of the main workflow that everything would be made available
automatically. The problem here was that I was forced by the instrument
software to do the analysis on a specific computer (that wasn't
networked) and that our LaBLog system has no means of multiple file
upload.

So to summarise the use case.

1.  Maria created four samples
2.  Original plan created to run the four samples plus backgrounds
3.  Realised 10mg/mL sample was aggregating and centrifuged to clear it
    (new unexpected procedure)
4.  Ran one of the pre-made samples three times, first time wasn't
    confident, second time was a failure, third time confirmed first
    time was ok
5.  New samples prepared from cleared 10 mg/mL sample
6.  Prepared two new samples from cleared 10 mg/mL sample
7.  Re-worked plan for running samples based on time available
8.  Ran 1 mg/mL sample for different amount of time than previous
    samples
9.  Ran remaining samples for various amounts of time
10. Data was collected from each sample after it was run and converted
    to a two column text format
11. Two column data was rebinned and background subtracted (this is
    where I went wrong with some of them, forgetting that in some cases
    I had two lots of electronic background)
12. Subtracted data was rebinned again and then desmeared (the
    instrument has a slit geometry rather than a pinhole) to generate a
    new two column data file.

So, four original samples, and three unexpected ones were created. One
set of data collection led to nine raw data files which were then
recombined in a range of different ways depending on collection times.
Ultimately this generates four finalised reduced datasets, plus a number
of files along the way. Two people were involved. And all of this was
done under reasonable time pressure. If you look at the commit times on
the posts you will realise that a lot of these were written (or at least
submitted) rather late in the day, particularly the data analysis. This
is because the data analysis was offline, out of the notebook in
proprietary software. Not a lot that can be done about this. The other
things that were late were the posts associated with the 'raw'
datafiles. In both cases a major help would be a 'directory watcher'
that automatically uploads files and queues them up somewhere so they
are available to link to.

This was not an overly complicated or unusual experiment but one that
illustrates the pretty commonÂ  changes of direction mid-stream and
reassessments of priorities as we went. What it does demonstrate is the
essential messiness of the process. There is no single workflow that
traces through the experiment that can be applied across the whole
experiment, either in the practical or the data analysis parts. There is
no straightforward parallel process applied to a single set of samples
but multiple, related samples, that require slightly different tacks to
be taken with data analysis.Â  What there are, are objects that have
relationships. The critical thing in any laboratory recording system is
making the recording of both the objects, and the relationships between
them, as simple and as natural as possible. Anything else and the record
simply won't get made.


Two rather exciting things are happening at the moment. Firstly we have finally got the LaBLog system up and running at RAL (http://biolab.isis.rl.ac.uk). Not a lot is happening there yet but we are gradually working up to a full Open Notebook status, starting by introducing people to the system bit by bit.

Messaggi di Rogue Scholar

A use case scenario for Mark…a description of the first experiment on the ISIS LaBLog