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MUD transcript:  10-03-00

Web Authoring; Projects

Course room(s): PPS 

16:05:42  ClareS connects.

KevinO       PPS          Telnet   4m 57s   1m 26s
Wizard       Void         Telnet   4m 25s   4m 25s
RamananS     PPS          Telnet      41s      41s
ClareS       PPS          HTTP         0s       0s
AttilaR      PPS          HTTP      4m 6s   3m 38s
16:05:45  ClareS says "Hi"
16:05:58  RamananS says "hello"
16:06:03  ClareS says "sorry about the last time... Netscape crashed :("
16:06:18  ClareS says "are you happy to start now?"
16:06:29  KevinO says "yes"
16:06:36  AttilaR says "Yes."
16:07:09  RamananS says "of course,yes"
16:07:14  ClareS says "OK..."
16:07:37  ClareS says "there are three possibilities for this session (or of course we could discuss more than one of these topics)"
16:07:44  KevinO says "Clare, you were going to talk about the projects?"
16:07:51  ClareS says "we could talk about the web authoring material"
16:08:02  ClareS says "or (as Kevin says) the projects"
16:08:32  ClareS says "or you may even have some questions on bioinformatics, since the last BioMOO was cancelled due to the network"
16:09:13  ClareS says "does anyone want to start with a question on any of these subjects, and we'll take it from there?"
16:10:02  KevinO says "I have no questions, but I would like to hear about the projects"
16:10:27  RamananS says "Bio informatics- How much of the excellent but lengthy course should we know by heart....."
16:11:44  RamananS says "......Do we have to know about all those database search engines and thats all or do we have tpo know aboutmthr.."
16:12:24  AttilaR says "I think, the material on bioinformatics, the most important thing is practice, and to learn, in which problam which database to contact, the important ones."
16:12:41  ClareS says "OK, I'll answer Ramanan's question first and then go on to discuss the projects"
16:13:24  ClareS says (to AttilaR) "that is correct!  You don't need so much to know it all as to know where to look"
16:13:33  VijayK connects.
KevinO       PPS          Telnet  12m 48s   3m 31s
Wizard       Void         Telnet  12m 16s  12m 16s
RamananS     PPS          Telnet   8m 32s   1m 49s
ClareS       PPS          HTTP     7m 51s       9s
AttilaR      PPS          HTTP    11m 57s    1m 9s
VijayK       PPS          HTTP         0s       0s
16:14:05  RamananS says "...about the technical ()biochemical lab"
16:14:09  ClareS says "you need to know what type of database or program it would be best to use for a particular problem"
16:14:26  VijayK says "Hello!"
16:15:05  ClareS says "but as the main focus of this course is on protein structure, you will only need to know the basics of bioinfo"
16:15:05  AttilaR says (to VijayK) "Hello!"
16:16:09  AttilaR says (to ClareS) "Shall we learn something about protein folding?"
16:16:17  ClareS says (to VijayK) "Hello!"
16:16:42  ClareS says (to AttilaR) "yes, but not a great deal. The next section is on molecular forces"
16:16:53  ClareS says "(that will be out on Monday)"
16:17:15  VijayK says "I am looking forward to learning something about protein folding"
16:17:33  RamananS says "thank you .my question seems to have been answered and the coursr is getting to be interesting too"
16:17:34  ClareS says "is this all clear? If so I'll go on to talk about the projects and you can bring up any more scientific questions at the end"
16:17:47  VijayK says "Well it looks like it is not possible now"
16:18:15  ClareS says (to VijayK) "go on... if you have a question I'll try to answer it now"
16:18:36  VijayK says "Section 6 was very interesting"
16:19:47  VijayK says "What is the expnsion for HETATM?"
16:19:47  ClareS says (to VijayK) "thanks, I'm glad you found it so... go on??"
16:20:27  VijayK says "I am referring to the Full Entry 2OVO"
16:20:27  ClareS says (to VijayK) "it's Heteroatom: any atom that is *not* in an amino acid is called a heteroatom"
16:20:47  ClareS says "they are found in most PDB files"
16:20:50  VijayK says "What is its realtion to HOH?"
16:21:29  ClareS says "HETATM is used to refer to water molecules (HOH), atoms in ligands and occasionally in non-standard amino acids"
16:22:14  ClareS says "each water atom is just represented by a single het atom: the oxygen"
16:22:38  ClareS says "it's not possible to resolve the positions of hydrogen atoms in water molecules around proteins"
16:22:42  VijayK says "well what is a nonstandard amino acid?"
16:23:00  ClareS says "any amino acid but the basic 20"
16:23:50  ClareS says "occasionally proteins are modified, either naturally or to make them easier to crystallise"
16:24:13  VijayK says "Reagrding CONNECT - do we have to look at a GIF to find the postions?"
16:24:54  ClareS says "you don't need to use these records, most programs don't need them now"
16:24:57  CharafB connects.
KevinO       PPS          Telnet  24m 12s  14m 55s
Wizard       Void         Telnet  23m 40s  23m 40s
RamananS     PPS          Telnet  19m 56s   7m 24s
ClareS       PPS          HTTP    19m 15s       3s
AttilaR      PPS          HTTP    23m 21s   8m 48s
VijayK       PPS          HTTP    11m 24s      44s
CharafB      PPS          HTTP         0s       0s
16:25:43  AttilaR says "What are the ways, the proteins can be made easier to crystallize?"
16:26:01  CharafB says "hello everyone, sorry for being late"
16:27:24  ClareS says (to CharafB) "welcome!"
16:27:41  ClareS says (to AttilaR) "that's really outside the scope of this course"
16:27:55  AttilaR says "But how do we know, the waters during crystallization are in the same position as in a simple water solution?"
16:28:35  VijayK says "About the section Movies of Protein Motions - I tried to view TATA-box, the image stays only for a second"
16:28:35  ClareS says "I'd recommend you to take one of our other Advanced Certificates, Protein Crystallography to find out more about this"
16:29:33  ClareS says (to AttilaR) "I'm not exactly sure what you mean -- you can see electron density for the oxygens of water molecules close to proteins"
16:30:43  ClareS says (to VijayK) "it's quite often difficult to view movies -- different platforms handle the file formats very slightly differently"
16:31:17  ClareS says "that's one reason why these movies are not used more often (another is file size)"
16:33:11  ClareS says "if there are no more burning questions I'd like to move on to the projects to give us plenty of time to discuss them"
16:33:29  ClareS looks round expectantly
16:34:02  VijayK says "Are we discussing the projects now?"
16:34:23  CharafB says "good idea!"
16:34:40  ClareS says "unless anyone is unclear about any of the previous answers"
16:34:58  AttilaR says "Yes, it is."
16:35:12  VijayK says "I am clear"
16:35:27  ClareS says "OK"
16:35:47  AttilaR says "We can talk the projects, I am clear."
16:36:02  ClareS says "well... we will post a list of projects on the web site in (about) early June"
16:36:24  ClareS says "you will be expected to select one of the fairly broad subject areas we suggest"
16:36:42  RamananS says "{"
16:36:52  RamananS says "since"
16:37:04  ClareS says "you write your project in HTML and submit it for late in October"
16:37:24  ClareS is not sure if this year's project submission date has been finally set yet
16:37:55  ClareS says "you will be given fairly detailed instructions for how and where to submit the projects"
16:38:28  ClareS says "when we post the project titles we will also tell you how they will be marked and give you pointers to some previous projects"
16:38:50  CharafB says "the timetable says 27/10/00 for submission of projects"
16:39:12  ClareS says "each of the projects linked from the PPS web site has reached at least a high enough standard to pass"
16:39:27  PaulW connects.
KevinO       PPS          Telnet  38m 42s  13m 14s
Wizard       Void         Telnet  38m 10s  12m 52s
RamananS     PPS          Telnet  34m 26s      42s
ClareS       PPS          HTTP    33m 45s      15s
AttilaR      PPS          HTTP    37m 51s   3m 40s
VijayK       PPS          HTTP    25m 54s   4m 15s
CharafB      PPS          HTTP    14m 30s      37s
PaulW        PPS          HTTP         0s       0s
16:39:27  ClareS says (to CharafB) "thanks!"
16:39:44  ClareS says (to PaulW) "welcome!"
16:40:49  ClareS says (to PaulW) "we're discussing the projects..."
16:40:52  AttilaR says (to ClareS) "Are we going to have another self-assessment period or an exam till then?"
16:41:08  ClareS says (to PaulW) "I've just run through the basic project procedure and time scale"
16:41:37  ClareS says (to AttilaR) "there will be another self assessment period after section 8 - it coincides with the easter holiday ;)"
16:42:18  ClareS says "so you can amuse yourself with answering questions about protein structure while eating chocolate eggs"
16:42:37  AttilaR says (to ClareS) "Thank You!"
16:43:15  VijayK says "Good idea"
16:43:32  RamananS says " OR"
16:44:02  RamananS says " I AM SORRY I CANNOT STOP SAYIN'Or' all the time....."
16:44:28  RamananS says "Will there be abny projects on databases...."
16:44:30  VijayK says "Or"
16:44:54  AttilaR says (to ClareS) "And what are the main topics of projects, just a few example to have an idea a bout it"
16:45:22  RamananS says "i mean constructing your own bioinformatic tool or something cool like that...."
16:45:35  ClareS says "you should know the date of the exam already"
16:45:56  ClareS says (to RamananS) "there should be a few projects on databases: mainly structural ones"
16:46:38  KevinO says (to ClareS) "where is the date of the exam specified?"
16:46:57  RamananS says "what exam?"
16:47:01  ClareS says (to RamananS) "there is (I suppose) nothing to stop you writing a bioinfo tool provided that it is accessible via a web browser and doesn't need any extra software to run"
16:47:30  KevinO says (to ClareS) "- I thought we needed to make arrangements locally about it (exam)?"
16:47:39  ClareS says "also we can't give you any extra credit for this -- we are testing your knowledge of protein structure not your programming ability"
16:48:27  ClareS says (to KevinO) "Annie will be contacting you all later in the year to find out whether you want to take the exam & help you make arrangements"
16:48:40  PaulW says " i have to go .sorry the visit was so short"
16:49:03  VijayK says "Bye Paul"
16:49:22  PaulW disconnects.
KevinO       PPS          Telnet  48m 37s   1m 52s
Wizard       Void         Telnet   48m 5s      56s
RamananS     PPS          Telnet  44m 21s   2m 25s
ClareS       PPS          HTTP    43m 40s      55s
AttilaR      PPS          HTTP    47m 46s   4m 28s
VijayK       PPS          HTTP    35m 49s      19s
CharafB      PPS          HTTP    24m 25s  10m 32s
16:49:53  ClareS says "Paul can catch up by reading the transcript later"
16:51:07  CharafB says "Are we going to have some supervision for the project or do you think the course material will be sufficient?"
16:52:29  ClareS says "you will not hava any formal supervision for the project"
17:00:44  ClareS says "there should be enough project titles to satisfy all interests (related to protein structure, that is)"
17:00:56  ClareS will be finishing soon and going for tea
17:01:16  RamananS says "thank you fpr yopur patience."
17:01:23  KevinO would prefer lunch
17:01:29  VijayK says "its good to know in advance so we will be prepared according to individual intersts"
17:01:39  ClareS says "All I am saying is that, we don't aim to teach people to program on this course, so we can't give people extra credit for being able to!"
17:01:42  AttilaR says "I have to go now, see You soon, in the next MUD-session."
17:02:15  ClareS says "if you do write a really good program (which would be difficult given the time allowed)..."
17:02:44  ClareS says "...my advice would be to recommend you to write it up for publication elsewhere"
17:02:49  VijayK says "Thank Clare. Loking forward for the next section on Monday"
17:02:53  ClareS says "like in the journal Bioinformatics"
17:03:31  VijayK says "Bye everybody"
17:03:31  ClareS says "however, even a bioinformatics project should be structure-based"
17:03:56  AttilaR says "Good bye!"
17:04:20  RamananS says "I fully understand the str. of prteins being the core."
17:04:59  KevinO 's hunger gets the better of him
17:05:48  VijayK disconnects.