Biomoo Held on the 29th Jul 99

ClareS turns the ClareS_recorder on.

ClareS says "hello and welcome to the first BioMOO for a little while: I'm really sorry about the technical hitches"

ClareS says "you have a choice: would you like to discuss the projects, or are there questions about the course material you'd like to raise?"

Nada says " I would like to talk about projects"

Gmocz says "OK with me."

ClareS says "fine: anyone else have any preferences?"

ClareS says "have you chosen your project titles yet?"

Gmocz [to ClareS] Yes. Use of fluorescence in protein tesearch

Gmocz [to ClareS] t>r

Nada says " No not yet I was hoping I could do something more Bioinformaticy"
ClareS has been loading Netscape 4 onto a borrowed slow Mac

ClareS says "there are one or two bioinformatics related projects, but I agree that the emphasis is not there"

ClareS says "there are some based round fold recognition which is quite close to "bioinformatics" - however that is defined"

Nada says " I was thinking something along the lines of Protein domains using Psi-BLAST"

Nada says " or HMMs but that can get quite scarey!"

ClareS says "we can't give people free choice of projects, in case anyone just puts HTML tags round the first chapter of their thesis"

ClareS says "of course, we know you won't, but *someone* might"
ClareS . o O ( I doubt anyone at Birkbeck has the expertise to mark a project on HMMs )

Nada says " the project entitled A comparison of Methods for discriminating between Protein Domains sounds roughly like waht I would like to do, but I am not sure what methods it involves"

ClareS says "it's at least partly up to you..."

ClareS says "examine a number of (free, web based) algorithms used for finding domains and domain boundaries - do they all give the same results? Do the domain boundaries seem to be biologically reasonable? How do sequence based and structure based methods compare?"

Nada says "that sounds good"

ClareS says "does that agree with what you had in mind?"

ClareS says "anyone else want to query anything about project choice?"

ClareS says "project work starts officially on 9 August..."

ClareS says "... but I should add that it's very easy to spend too long on the project and forget to revise for the exam"

Gmocz [to ClareS] Fluorescence is a large subject. What do you think I have to concentrate on in relation to proteins? Of course its up to me .. but
ClareS . o O ( but? )

Gmocz [to ClareS] Any suggestion?

ClareS says "how fluorescence is used.. Green fluorescence protein and its variants, structure, function, and mechanism, ..."

Gmocz [to ClareS] All these were in mind. How about use of external use of external labels, such as fl. labelled substrates?

ClareS says "yes, of course -- but stick to applications related to protein structure"

ClareS says "with GFP, of course, you're using a protein to probe the structure of a protein"

Gmocz [to ClareS] like measuring distances in proteinS?

Gmocz [to ClareS] GFP is a clear case

ClareS [to gmocz] yes, of course

ClareS says "you will be given full instructions for submitting your projects in due coure"
ClareS . o O ( course )

ClareS says "basically you will be expected to produce a single archive (.tar.gz, .zip or whatever) from all your files and email this to Dave Houldershaw"

Gmocz [to ClareS] what is the minimum and maxumum size of a projext that is acceptable?

ClareS says "there are no minimum and maximum sizes "

ClareS says "have a look through last year's projects, and the year before's, to see the kind of thing we're looking for - all the projects on the Web site passed"

ClareS says "the minimum spec. can probably be gauged from there - the maximum will be determined by the amount of time that can reasonably be spent on a project"

ClareS says "given that you have an exam to revise for, and a day job ;)"

Gmocz [to clare] I have the same sad feeling about that too. Especially about the daily work

ClareS says "yes, that's why we don't expect a huge project"

Gmocz [to ClareS] What is the deadline to turn the project in?

ClareS says "end October - about the 24th but I can't remember the exact date"

Gmocz [to ClareS] that is good enough for now. I got the idea.

ClareS says "do remember that we won't be expecting you to know web programming"

ClareS says "just enough HTML to be able to get the scientific concepts across clearly and attractively"

ClareS says "are there any more questions on the projects.. or on the course material??"
ClareS . o O ( sections 10, 11 or 12 - it's a long time since the last session )

Gmocz [to ClareS] Are we supposed to use a plain text editor, or we can use an HTML editor to speed things up? Gmocz [to ClareS]: So I mean what is the meaning of 'enough HTML"

ClareS says "you can use whatever software you like to generate the code - we won't know"

ClareS says "you're expected to make intelligent use of images and of links (within and outside your material)"

ClareS says "not - necessarily - to know perl or javascript, let alone java"

ClareS says "rasmol and/or chime is practically essential in this area, of course"
Gmocz (HTML editors usually put their mark/ID somewhere near the heading)

ClareS says "yes, but we're not that devious ;) - and HTML can always be edited"
Gmocz (Of course that is not displayed)
Gmocz OK, OK I am not really serious on this
ClareS grins

Gmocz [to ClareS] If there is nothing else about the projects then I have a question referring back to section 9.In X-ray crystallography, the quality of a protein structure is judged by the resolution and refinement-factor. These parameters have no meaning in NMR determinations. What parameters or indices can be used to judge a NMR derived structure?
ClareS . o O ( section 9 was a while ago.. )

ClareS says "how well satisfied the NMR restraits are"

ClareS says "plus the "quality" of the structure - how well bond lengths, angles etc. compare with standard values - this goes for any structure"
(Nada has disconnected.)

Gmocz [to ClareS] What NMNR restraints?
Gmocz NMR

ClareS says "proton-proton distances (the raw data from 2D NMR experiments)"

Gmocz [to ClareS] All right, now it is clear. I always wanted to clarify this question but we had no meeting for a while. Thanks.

ClareS says "sorry -- I admit BioMOO has had some technical problems :("

ClareS says "it does seem to be running smoothly today"
The housekeeper arrives to cart Nada off to bed.

Gmocz [to ClareS] Only 11 of 65 theoretically possible crystal forms for proteins have been observed so far. Do you think that more forms will be found later with new structures, or ~11 is some kind of limit or restriction caused by some feature of protein structure itself?

ClareS says "protein structure geometry limits the crystal forms that proteins can take up"
Gmocz So the 230 forms goes down to 65 Gmocz in "real" life to 11?

ClareS says "I don't know whether there are still one or two forms still to be discovered in proteins, or whether we've found all that can be observed"

ClareS says "I must point out that I *must* leave by 17:30BST (in 15 mins or so)"
Gmocz Maybe a few more ? Only a small percentage of proteins have Xray structure so far
Gmocz Anyway we shall see in the (near?) furure

ClareS says "you really need an expert in symmetry to answer that one (I'm not ;)"
Gmocz but it may be some additional restriction that brings the number down to a dozen or so

ClareS says "there's something on this in section 11, under Symmetry... or if you're still keen to learn more you could follow PPS with our Protein Crystallography course - there's *much* more on symmetry in that one"
Gmocz I am thinking about that too. But perhaps not this year, but a year after
Gmocz Its is past 6 am here. I will have to go to work in a few minutes.
ClareS . o O ( another one of us... very late ;) )
Fulvio finds his way in.

ClareS [to gmocz] thank you for your lively contributions to the meeting - especially as it's so early in Hawaii ;)

ClareS [to Fulvio] hi, welcome ... did you realise you're 90 minutes late?
ClareS . o O ( nearly, at least.. )

Gmocz [to Fulvio] Hello!

Fulvio says "hello to all"

Fulvio says "I,m very sorry"

Fulvio says "I was in a trafic jam!!!"

Fulvio says "Not in an electronic one"

ClareS says "I'm *very* sorry..."

ClareS says "especially as BioMOO has been in an electronic traffic jam the last couple of times we tried to hold meetings"

Fulvio says "I try to read the tape of the today's session"

Gmocz [to Fulvio] I will be in a traffic jam very soon. It takes nearly 2 hours to commute to work in the morning. It is only 20 miles

Fulvio says "I live in Rome, and the Jubileum is a terrible event for us"

Fulvio says "because THEY are trying to solve all the problem in a few time"
ClareS . o O ( not like my mental picture of Hawaii, at all ;) )

Fulvio says "I thought that Hawaii is made of little islands"

Gmocz [to ClareS] After 9 am is OK But morning and evening commuting is teruble due to linited highway system

ClareS [to Fulvio] can I suggest that you read the transcript (jul29tape) and email me with any questions.. I really *must* go very soon

Gmocz [to Fulvio] they are little comparing to the Mainland but big enough to have traffic jams

Fulvio says "OK, i'm mailing me the transcript"
ClareS turns the ClareS_recorder off.