MUD transcript: 09-02-00
Introduction to Bioinformatics
Please note that this MUD session was held during the Department of
Crystallography's successful Subject
Review. Many thanks to those students who managed to seamlessly combine taking part in a
bioinformatics tutorial with answering the questions posed by our assessor, Dr.
Robert Glass.
15:05:02 SpyrosS connects.
15:05:02
LarryT PPS Telnet 11m 13s 4m 23s
MonikaS PPS HTTP 14m 1s 5m 34s
CharafB PPS HTTP 13m 51s 3m 10s
BartoszB PPS HTTP 6m 44s 6m 44s
ClareS PPS HTTP 6m 37s 5m 31s
IJT PPS HTTP 10m 32s 23s
RobertO PPS HTTP 10m 12s 1m 20s
MichaelS PPS HTTP 6m 33s 1m 2s
VijayK PPS HTTP 1m 20s 18s
SpyrosS PPS HTTP 0s 0s
15:05:17 ClareS says "I'm back... and we are ready to go"
15:05:22 MichaelS says (to ClareS) "Sorry about that fals call for help. I was trying to send you a to message."
15:05:51 ClareS says "I'm very pleased to see so many of you here"
15:05:51 SpyrosS says "Hello everyone"
15:05:54 IJT says (to SpyrosS) "Hi we haven't started yet - Clare's not here (physically I mean)."
15:05:59 Glass connects.
15:05:59
LarryT PPS Telnet 12m 10s 5m 20s
MonikaS PPS HTTP 14m 58s 6m 31s
CharafB PPS HTTP 14m 48s 4m 7s
BartoszB PPS HTTP 7m 41s 23s
ClareS PPS HTTP 7m 34s 8s
IJT PPS HTTP 11m 29s 5s
RobertO PPS HTTP 11m 9s 2m 17s
MichaelS PPS HTTP 7m 30s 37s
VijayK PPS HTTP 2m 17s 1m 15s
SpyrosS PPS HTTP 57s 8s
Glass PPS HTTP 0s 0s
15:06:15 IJT says (to Glass) "Hi"
15:06:17 ClareS says "we are ready so start now"
15:06:20 Glass says "Hello everybody"
15:06:32 MichaelS says (to IJT) "Sorry about that Ian, I was going to tell Clare that I might have to disconnect at any time because I am not at my usual machine."
15:06:41 ClareS says "I'd like to start by welcoming you all to this special MUD"
15:07:19 ClareS says "before we start with Bioinformatics, may I introduce Dr Robert Glass (username Glass) who is one of our assessors"
15:07:19 Glass says " A quick description of QAA. We are here to find out about the student experience."
15:07:39 ClareS says "he will be asking you a few questions as we go along"
15:07:58 ClareS says "firstly, could a few of you introduce yourselves?"
15:08:00 Glass says " So we are very interested in thi snovel form of education."
15:08:24 ClareS says (to RobertO) "and remember to add *where* you are from and *what time it is* for you ;)"
15:08:42 Glass says "First question: Do you find you can manage without textbooks?"
15:09:02 BartoszB disconnects.
15:09:02
LarryT PPS Telnet 15m 13s 2s
MonikaS PPS HTTP 18m 1s 9m 34s
CharafB PPS HTTP 17m 51s 1m 44s
ClareS PPS HTTP 10m 37s 19s
IJT PPS HTTP 14m 32s 2m 47s
RobertO PPS HTTP 14m 12s 5m 20s
MichaelS PPS HTTP 10m 33s 19s
VijayK PPS HTTP 5m 20s 1m 26s
SpyrosS PPS HTTP 4m 0s 3m 11s
Glass PPS HTTP 3m 3s 20s
15:09:16 RobertO says "HI, I am Robert and live near San Francisco California and it is a wet rainy morining here."
15:09:48 MichaelS says "Good afternoon, Dr Glass. My name is Mike Swanton, I'm from Australia but working in London, at LGC Ltd (the former Government Chemist)."
15:09:51 LarryT says "It's 10 am here in Ann Arbor, Michigan. I am a biochemist here"
15:09:52 Glass says "Second questions: Do you find that MUD is an efficient form of communication?"
15:10:24 MonikaS says "I come from Poland. I am fourth year student of farmacy in Poznan. It's 4 pm here."
15:10:38 BartoszB connects.
15:10:38
LarryT PPS Telnet 16m 49s 47s
MonikaS PPS HTTP 19m 37s 14s
CharafB PPS HTTP 19m 27s 3m 20s
BartoszB PPS HTTP 0s 0s
ClareS PPS HTTP 12m 13s 1m 55s
IJT PPS HTTP 16m 8s 4m 23s
RobertO PPS HTTP 15m 48s 1m 22s
MichaelS PPS HTTP 12m 9s 50s
VijayK PPS HTTP 6m 56s 3m 2s
SpyrosS PPS HTTP 5m 36s 4m 47s
Glass PPS HTTP 4m 39s 46s
15:10:51 ClareS says "this is excellent!"
15:11:08 CharafB says "Hello, I am from the Royal Veterinary College in London"
15:11:10 ClareS wonders what our mean distance from Birkbeck College is
15:11:12 RobertO says "I am a spectroscopist and engineer and work in a computational chemistry group and for me it is just past 7am."
15:11:15 LarryT says "I have printed reams of material from this class .. in many ways, this is more current than a printed text ...printed text supplement the web-obtained material"
15:11:45 SpyrosS says "Hi I am Spiros. I am in Birkbeck! I am a physicist trying to do research in biochemistry"
15:12:00 ClareS says "so you see you *can* read our material on the train... if you have a good printer"
15:12:12 Glass says "I am a bacterial geneticist who first trained as a chemist, then did a PhD on NGF and finally settled for bacterial genetics. I am based in Nottingham (in the midlands, UK) in the Institute of Genetics."
15:12:51 MichaelS says "Q1. Even if I was at a face-to-face course, I would have other texts, so in that way, things aren't all that different. I suppose the one big issue with this kind of course is the problem of the slower speed of moving about cyberspace compard with the hpysical world. Having said that, it might be my lack of experience that slows things down!!"
15:13:00 BartoszB says "Hello I am Bartosz Balana. I am studying pharmacy in Poznan, Poland. Here is afternoon, about 4 pm"
15:13:32 LarryT says "MUD works for me ... I am using it instead of a browswer 'cause there is no graphics delay ... the ONLY problem is it does not have spell check to correct my lack of typing skill (g)"
15:13:40 RobertO says "I find my fast color printer gives me time to read the web pages over on my long commute after I have initially gone through online. I also love the ability to interact with the material with rasmol and the other programs to help visualize."
15:13:57 ClareS says "no-one can type *quite* as fast as they can talk... I'm working on it, but I make a lot of typing errors"
15:14:46 RobertO says "I also supplement the web information with several texts since I am new to the biology and it takes me a little longer to fill in all my background needs."
15:14:59 MichaelS says "MUDs are quite helpful, once you get used to the format."
15:15:06 CharafB says "A lot of the learning we have done until now using molecule viewers could a lot more difficult with books"
15:15:45 ClareS says "this form of communication does take a bit of getting used to"
15:15:58 Glass says "re Q1, if you do use texts, don't you think that people who have access to these might find the web-based course easier therefore?"
15:16:12 MichaelS says "I certainly agree about the graphics and molecular visualisations So much easier to get 3-dimensional concepts."
15:16:26 ClareS says "but once you're used to it, I find that it's straightforward to use"
15:16:27
LarryT PPS Telnet 22m 38s 2m 55s
MonikaS PPS HTTP 25m 26s 6m 3s
CharafB PPS HTTP 25m 16s 1m 21s
BartoszB PPS HTTP 5m 49s 3m 27s
ClareS PPS HTTP 18m 2s 1s
IJT PPS HTTP 21m 57s 0s
RobertO PPS HTTP 21m 37s 1m 41s
MichaelS PPS HTTP 17m 58s 15s
VijayK PPS HTTP 12m 45s 51s
SpyrosS PPS HTTP 11m 25s 4m 42s
Glass PPS HTTP 10m 28s 29s
15:17:19 Glass says "I can see why the web is great for a structural course - of course."
15:17:59 VijayK disconnects.
15:17:59
LarryT PPS Telnet 24m 10s 4m 27s
MonikaS PPS HTTP 26m 58s 7m 35s
CharafB PPS HTTP 26m 48s 2m 53s
BartoszB PPS HTTP 7m 21s 4m 59s
ClareS PPS HTTP 19m 34s 1m 33s
IJT PPS HTTP 23m 29s 11s
RobertO PPS HTTP 23m 9s 3m 13s
MichaelS PPS HTTP 19m 30s 1m 47s
SpyrosS PPS HTTP 12m 57s 6m 14s
Glass PPS HTTP 12m 0s 40s
15:18:23 MichaelS says "I suppose that I use the texts I have in the same way as I would otherwise, to consolidate teaching material, and see if I can answer questions before they come up in a tutorial/MUD style forum."
15:18:43 ClareS says "what do the rest of you think of the MUD as a communication tool?"
15:18:50 SpyrosS says "For me it important to study at my own pace. I have a lot of new material to learn, and going to lectures isn't something I would prefer."
15:19:01 RobertO says " I find it need a good road map and overview in a class so I can see the path to be on when I dont know the subject , then I can help with some details with the text and also use the wonderful visualization of this course to clarify what the text cannot."
15:19:23 ClareS says (to SpyrosS) "and that is one of the benefits of this course for you?"
15:19:36 Glass says "Question 3: do you have quidelines for your project?"
15:19:48 RobertO says "also the mud allows the feel of participating with classmates and interacting with questions."
15:20:28 SpyrosS says (to ClareS) "Yes it is"
15:20:41 VijayK connects.
15:20:41
LarryT PPS Telnet 26m 52s 14s
MonikaS PPS HTTP 29m 40s 10m 17s
CharafB PPS HTTP 29m 30s 20s
BartoszB PPS HTTP 10m 3s 7m 41s
ClareS PPS HTTP 22m 16s 1m 18s
IJT PPS HTTP 26m 11s 2m 53s
RobertO PPS HTTP 25m 51s 53s
MichaelS PPS HTTP 22m 12s 2m 18s
VijayK PPS HTTP 0s 0s
SpyrosS PPS HTTP 15m 39s 13s
Glass PPS HTTP 14m 42s 1m 5s
15:20:41 ClareS says "I had better answer the question about the project: we haven't issued the guidelines yet because it's too early in the course for that"
15:21:15 ClareS says "they will be available after Easter"
15:21:16 CharafB says "The MUD and the email are really necessary to clarify some points"
15:21:20 MichaelS says "sorry, must go. I'll try to reconnect in a couple of minutes."
15:21:30 MichaelS disconnects.
15:21:30
LarryT PPS Telnet 27m 41s 14s
MonikaS PPS HTTP 30m 29s 11m 6s
CharafB PPS HTTP 30m 19s 14s
BartoszB PPS HTTP 10m 52s 8m 30s
ClareS PPS HTTP 23m 5s 15s
IJT PPS HTTP 27m 0s 3m 42s
RobertO PPS HTTP 26m 40s 1m 42s
VijayK PPS HTTP 49s 12s
SpyrosS PPS HTTP 16m 28s 1m 2s
Glass PPS HTTP 15m 31s 1m 54s
15:22:02 ClareS says "we will be starting to do some bioinformatics quite soon"
15:22:43 ClareS says (to Glass) "the transcript will be very important for someone like Michael who has to leave in the middle of a session"
15:22:46 RobertO says "I also feel that the flexible study time is so important since my job is very demanding and I live so far from work. This makes it impossible for me to attend a regular class."
15:23:01 Glass says "Finally question(at the moment! to you all), do you understand what the differeent forms of the Advancesd certificate mean? i.e. the Advanced certififcate, the certificate of participation etc?"
15:23:01 BartoszB says "Course material are good enough to learn without handbook. And of corse there is a lot of recommended books at the end of each section. The favour of Internet course is posibilty to interact with diffrent kind of materials and it's very easy to follow the hyperlink to find other. The MUD is a useful way of communications, but I am not a fast type-writer so sometimes i don't follow. Moreover I still got some technical problems just becouse of poor and unstable connections I am using"
15:24:40 ClareS says "the ability to link to other places in the Web is particularly valuable in the section we're currently doing: Bioinformatics"
15:24:56 Glass says (to BartoszB) "Yes, I am a pretty poor typist and |I can get quite frustrated!"
15:25:23 ClareS says "can I repeat Dr Glass' question: do you understand what you have to do to get the different types of certificate?"
15:25:39 VijayK disconnects.
15:25:39
LarryT PPS Telnet 31m 50s 1m 5s
MonikaS PPS HTTP 34m 38s 15m 15s
CharafB PPS HTTP 34m 28s 4m 23s
BartoszB PPS HTTP 15m 1s 2m 38s
ClareS PPS HTTP 27m 14s 16s
IJT PPS HTTP 31m 9s 47s
RobertO PPS HTTP 30m 49s 2m 53s
SpyrosS PPS HTTP 20m 37s 5m 11s
Glass PPS HTTP 19m 40s 43s
15:25:54 ClareS says "I think we had better move on to Bioinformatics now, but we'd still like a few more answers to some of Dr Glass' questions"
15:25:55 RobertO says "yes I believe I understand, one says you were here and participated but did not participate and pass a written exam while the other is given for completing the written exam successfully and also a project."
15:25:56 MichaelS connects.
15:25:56
LarryT PPS Telnet 32m 7s 1m 22s
MonikaS PPS HTTP 34m 55s 15m 32s
CharafB PPS HTTP 34m 45s 4m 40s
BartoszB PPS HTTP 15m 18s 2m 55s
ClareS PPS HTTP 27m 31s 2s
IJT PPS HTTP 31m 26s 1m 4s
RobertO PPS HTTP 31m 6s 1s
MichaelS PPS HTTP 0s 0s
SpyrosS PPS HTTP 20m 54s 5m 28s
Glass PPS HTTP 19m 57s 1m 0s
15:25:56 VijayK connects.
15:25:56
LarryT PPS Telnet 32m 7s 1m 22s
MonikaS PPS HTTP 34m 55s 15m 32s
CharafB PPS HTTP 34m 45s 4m 40s
BartoszB PPS HTTP 15m 18s 2m 55s
ClareS PPS HTTP 27m 31s 2s
IJT PPS HTTP 31m 26s 1m 4s
RobertO PPS HTTP 31m 6s 1s
MichaelS PPS HTTP 0s 0s
VijayK PPS HTTP 0s 0s
SpyrosS PPS HTTP 20m 54s 5m 28s
Glass PPS HTTP 19m 57s 1m 0s
15:26:23 ClareS says "please interrupt the tutorial when you have something to say to him"
15:26:24 LarryT says "As I understand it, I need to complete assigments, do a project and take a final proctored exam for "advanced Cert""
15:27:00 CharafB says "I would agree with Robert and Larry who typed faster!"
15:27:09 ClareS says "welcome back, Michael and Vijay"
15:27:42 BartoszB says (to Glass) "I read the information about the certificates and I supose to know what i have to do to achieve one of this certificates"
15:28:07 ClareS says "so, how have you been finding the Bioinformatics course material?"
15:29:08 BartoszB says "Bioinformatics material was great I see"
15:29:09 AttilaR connects.
15:29:09
LarryT PPS Telnet 35m 20s 2m 45s
MonikaS PPS HTTP 38m 8s 18m 45s
CharafB PPS HTTP 37m 58s 2m 9s
BartoszB PPS HTTP 18m 31s 1s
ClareS PPS HTTP 30m 44s 17s
IJT PPS HTTP 34m 39s 9s
RobertO PPS HTTP 34m 19s 3m 14s
MichaelS PPS HTTP 3m 13s 13s
VijayK PPS HTTP 3m 13s 1m 9s
SpyrosS PPS HTTP 24m 7s 8m 41s
Glass PPS HTTP 23m 10s 4m 13s
AttilaR PPS HTTP 0s 0s
15:29:13 ClareS says "I know that this session is only a couple of days after the material was released"
15:29:24 CharafB says "It is very well presented with a lot of very intersting links and useful softwares"
15:29:26 ClareS says (to AttilaR) "welcome!"
15:29:39 VijayK says "To Clare's question\; Had been reading the portions for this afternoon"
15:29:51 MonikaS says "It is very interesting, but I haven't enough time to do all the exercises yet."
15:29:55 ClareS says "... but have you been able to explore the tutorial yet?"
15:30:01 AttilaR says "Good Afternoon!"
15:30:14 ClareS says "who would like to start with a question on bioinformatics?"
15:30:36 VijayK says "It's been Great! I would be particularly interested in the homology bits in future"
15:30:37 MichaelS says "there certainly is a lot of information in it. Ittook a bit of time to get around the windows."
15:30:44 ClareS says (to AttilaR) "I would like to introduce our assessor -- Dr Robert Glass. Could you introduce yourself?"
15:30:49 RobertO says "truthfully Clare this week so far has been very hectic for me and since it is not a print and read on the train I must say I havent delved in deeply yet. The section looks good since it has the practical feel that allows you to interact but I will know later this week. This is one of the features I like about this course. I can do it at my pace and schedule."
15:31:07 BartoszB says "The bioinformatic material was excellent. I like the tutorial very much"
15:31:24 ClareS says "how much did you know about protein sequence analysis before starting this section?"
15:31:47 AttilaR says "Yes, of course, my name is Attila Racz, I am from Hungary. Sorry, for being late."
15:31:56 ClareS says (to RobertO) "very true.. you can't print this section out and read it on the train"
15:32:16 CharafB says "I think that to master the different programs we will have to practice a lot, but at least we will know were to look for these, and what is possible to achieve."
15:32:57 ClareS says "OK, *I'll* start off with a question. Can someone tell me the exact definition of the word "homology"?"
15:34:15 ClareS looks round expectantly...
15:34:31 ClareS looks round expectantly...
15:34:56 RobertO says "For me all this is probably a little harder since my initial background is engineering and programming and I must work harder on the concepts and fill in gaps that many dont have. BUT I feel this course is doing an excellent job and directing me, so I can spend more time concentrating in a focused manner."
15:35:11 BartoszB says "I know a little about experimental part of sequence analysis, but a very little about data processing. I know that there are database , but I didn't realise that they are so quick and easy accessible.I am impressed."
15:35:13 LarryT says "sequences related from a common ancestor, as opposed to "similar""
15:35:16
LarryT PPS Telnet 41m 27s 3s
MonikaS PPS HTTP 44m 15s 5m 25s
CharafB PPS HTTP 44m 5s 3m 0s
BartoszB PPS HTTP 24m 38s 5s
ClareS PPS HTTP 36m 51s 29s
IJT PPS HTTP 40m 46s 4m 33s
RobertO PPS HTTP 40m 26s 20s
MichaelS PPS HTTP 9m 20s 1m 21s
VijayK PPS HTTP 9m 20s 3m 39s
SpyrosS PPS HTTP 30m 14s 14m 48s
Glass PPS HTTP 29m 17s 0s
AttilaR PPS HTTP 6m 7s 3m 29s
15:35:20 VijayK says "Def Homology: Sequences are said to be homologous if they are related by divergence from a common ancestor (Preface)"
15:35:39 MichaelS says "As I understand it, homology is sito identity, but in a functional sense, rather than a strict sequence-based sense."
15:35:49 SpyrosS says "proteins with amino acid similarity that indicates a common ancestor"
15:35:58 RobertO says "I would say degree of similarity is a short definition"
15:36:08 ClareS says "yes, the important point about homology is that homologous sequences are *as far as can be determined* derived from a common ancestor"
15:36:39 ClareS says "you can have "similar" sequences that are not homologous, like some of the TIM barrels"
15:37:10 VijayK says "What are TIM barrels?"
15:37:15 ClareS says "if you define sequences as homologous they must be similar enough for the evolutionary relationship to be clear"
15:37:19 SarahL connects.
15:37:19
LarryT PPS Telnet 43m 30s 2m 6s
MonikaS PPS HTTP 46m 18s 7m 28s
CharafB PPS HTTP 46m 8s 1m 54s
BartoszB PPS HTTP 26m 41s 2m 8s
ClareS PPS HTTP 38m 54s 4s
IJT PPS HTTP 42m 49s 6m 36s
RobertO PPS HTTP 42m 29s 1m 21s
MichaelS PPS HTTP 11m 23s 1m 40s
VijayK PPS HTTP 11m 23s 9s
SpyrosS PPS HTTP 32m 17s 1m 30s
Glass PPS HTTP 31m 20s 2m 3s
AttilaR PPS HTTP 8m 10s 5m 32s
SarahL PPS HTTP 0s 0s
15:37:57 AttilaR says "How do we know, which similar sequences are homologous?"
15:37:57 ClareS says (to VijayK) "one particular type of protein fold -- you'll be studying them later. Many unrelated proteins have the same fold"
15:38:46 SarahL says "hi just arrived sorry I'm late"
15:38:58 ClareS says "you can't say that 2 proteins are 50% homologous -- if you did, you'd probably mean that they were 50% similar"
15:39:13 ClareS says "sequences are either homologous, or they are not"
15:39:40 ClareS says (to SarahL) "don't worry about being late, and thanks for your email"
15:39:47 VijayK says "I note that protein folds are referres to in assigning the analogous types"
15:40:18
LarryT PPS Telnet 46m 29s 5m 5s
MonikaS PPS HTTP 49m 17s 10m 27s
CharafB PPS HTTP 49m 7s 4m 53s
BartoszB PPS HTTP 29m 40s 5m 7s
ClareS PPS HTTP 41m 53s 38s
IJT PPS HTTP 45m 48s 0s
RobertO PPS HTTP 45m 28s 2m 23s
MichaelS PPS HTTP 14m 22s 4m 39s
VijayK PPS HTTP 14m 22s 31s
SpyrosS PPS HTTP 35m 16s 4m 29s
Glass PPS HTTP 34m 19s 5m 2s
AttilaR PPS HTTP 11m 9s 2m 21s
SarahL PPS HTTP 2m 59s 1m 32s
15:40:20 ClareS says (to SarahL) "may I introduce Dr Robert Glass, our assessor -- maybe you could introduce yourself to him?"
15:41:34 Glass says (to SarahL) "hello, I am Robert."
15:41:54 ClareS says (to VijayK) "yes, that's right"
15:42:29 ClareS says (to VijayK) "could you type the URL you're looking at so that I have a clear idea of what you mean"
15:42:31
LarryT PPS Telnet 48m 42s 7m 18s
MonikaS PPS HTTP 51m 30s 12m 40s
CharafB PPS HTTP 51m 20s 1m 23s
BartoszB PPS HTTP 31m 53s 7m 20s
ClareS PPS HTTP 44m 6s 2s
IJT PPS HTTP 48m 1s 2m 13s
RobertO PPS HTTP 47m 41s 4m 36s
MichaelS PPS HTTP 16m 35s 6m 52s
VijayK PPS HTTP 16m 35s 2m 44s
SpyrosS PPS HTTP 37m 29s 6m 42s
Glass PPS HTTP 36m 32s 0s
AttilaR PPS HTTP 13m 22s 4m 34s
SarahL PPS HTTP 5m 12s 3m 45s
15:44:03 IJT says "I would suggested pasting is more reliable! If you make a typo we will get a bad link."
15:44:24 ClareS says "analogues are proteins that are similar due to convergent evolution -- they just happened to evolve with a particular sequence & structure as it's very efficient"
15:44:28 VijayK says "I am trying top find that bit"
15:44:38 SarahL says "hi Dr Glass , or Robert we seem to be on first names in the Mud, I'm Sarah Lee , I do research on Malaria mainly on the genome project@ the Institute of Molecular Medicine in Oxford, i work part time and I have 3 children, thats me in one sentence"
15:44:53 Glass disconnects.
15:44:53
LarryT PPS Telnet 51m 4s 9m 40s
MonikaS PPS HTTP 53m 52s 15m 2s
CharafB PPS HTTP 53m 42s 3m 45s
BartoszB PPS HTTP 34m 15s 9m 42s
ClareS PPS HTTP 46m 28s 29s
IJT PPS HTTP 50m 23s 50s
RobertO PPS HTTP 50m 3s 6m 58s
MichaelS PPS HTTP 18m 57s 9m 14s
VijayK PPS HTTP 18m 57s 25s
SpyrosS PPS HTTP 39m 51s 9m 4s
AttilaR PPS HTTP 15m 44s 6m 56s
SarahL PPS HTTP 7m 34s 15s
15:45:29 Glass connects.
15:45:29
LarryT PPS Telnet 51m 40s 10m 16s
MonikaS PPS HTTP 54m 28s 15m 38s
CharafB PPS HTTP 54m 18s 4m 21s
BartoszB PPS HTTP 34m 51s 10m 18s
ClareS PPS HTTP 47m 4s 1m 5s
IJT PPS HTTP 50m 59s 1m 26s
RobertO PPS HTTP 50m 39s 7m 34s
MichaelS PPS HTTP 19m 33s 9m 50s
VijayK PPS HTTP 19m 33s 1m 1s
SpyrosS PPS HTTP 40m 27s 9m 40s
Glass PPS HTTP 0s 0s
AttilaR PPS HTTP 16m 20s 7m 32s
SarahL PPS HTTP 8m 10s 51s
15:45:43 ClareS says "here's a harder question while Vijay looks for the link: what is the difference between a paralog and an ortholog?"
15:46:41 MichaelS says "I knew I should have aken Greek!:-)"
15:46:44 ClareS says "that may not even be in the tutorial, I'm interested to see whether you know"
15:47:10 VijayK says "the link: Http://boiinf.man.ac.uk/dbbrowser/bioactivity/theory.html"
15:47:39 ClareS says "there is a typo in that link, I *should* have asked you to paste it in"
15:48:03 ClareS says "it should be bioinf.man so the whole url is..."
15:48:18 IJT says "It still doesn't work."
15:48:46 ClareS says "http://bioinf.man.ac.uk/dbbrowser/bioactivity/theory.html"
15:49:07 VijayK says "Ortholog:when homologous proteins may perform the same functions in different species"
15:49:13 ClareS says "that was a guess..."
15:49:23 ClareS says (to VijayK) "excellent!"
15:49:28 IJT says (to ClareS) "Sorry that doesn't work either. Vijay can you check?"
15:49:56 MichaelS says "Doesn't para mean beside, and ortho means the same as?"
15:50:03 VijayK says "sorry about the typo ( iam hopeless in this matter). No it's not a guess"
15:50:56 BartoszB disconnects.
15:50:56
LarryT PPS Telnet 57m 7s 15m 43s
MonikaS PPS HTTP 59m 55s 3m 16s
CharafB PPS HTTP 59m 45s 9m 48s
ClareS PPS HTTP 52m 31s 1m 33s
IJT PPS HTTP 56m 26s 1m 28s
RobertO PPS HTTP 56m 6s 13m 1s
MichaelS PPS HTTP 25m 0s 1m 0s
VijayK PPS HTTP 25m 0s 53s
SpyrosS PPS HTTP 45m 54s 15m 7s
Glass PPS HTTP 5m 27s 5m 27s
AttilaR PPS HTTP 21m 47s 12m 59s
SarahL PPS HTTP 13m 37s 6m 18s
15:51:04 IJT says "Try http://bioinf.man.ac.uk/dbbrowser/bioactivity/"
15:51:07 BartoszB connects.
15:51:07
LarryT PPS Telnet 57m 18s 15m 54s
MonikaS PPS HTTP 1h 0m 3m 27s
CharafB PPS HTTP 59m 56s 9m 59s
BartoszB PPS HTTP 0s 0s
ClareS PPS HTTP 52m 42s 1m 44s
IJT PPS HTTP 56m 37s 3s
RobertO PPS HTTP 56m 17s 13m 12s
MichaelS PPS HTTP 25m 11s 1m 11s
VijayK PPS HTTP 25m 11s 1m 4s
SpyrosS PPS HTTP 46m 5s 15m 18s
Glass PPS HTTP 5m 38s 5m 38s
AttilaR PPS HTTP 21m 58s 13m 10s
SarahL PPS HTTP 13m 48s 6m 29s
15:51:14 ClareS says "I meant that mine was a guess."
15:51:24 VijayK says "http://bioinf.man.ac.uk/dbbrowser/bioactivity/theory.html2"
15:51:33 RobertO says "sorry I am being so quiet but I am in the listen and learn mode from the ones who have been in biology longer."
15:52:06 VijayK says "i think Iam wrong again"
15:52:22 IJT says (to VijayK) "No that doesn't work, try mine."
15:53:04 SpyrosS says (to MichaelS) "Yes but there are meanings also. e.g. ortho= the correct"
15:53:08 ClareS says "yes... Ian has typed the link for the tutorial front page. I was hoping that Vijay could type in one for a particular section..."
15:53:27 VijayK says "http://bioinf.man.ac.uk/dbbrowser/bioactivity/"
15:53:34 ClareS says "I think we can manage without the page open for now"
15:53:58 MichaelS says "If Vijay's definition of ortholog is right, does that mean we are subdividing so-called homologous proteins?"
15:54:35 ClareS says "orthologs are "the same" protein (with the same function) in two different species"
15:54:51 CharafB says "What is the exact difference between the two non-redundant database OWL and NRDB?"
15:55:09 ClareS says "paralogs are related proteins that have evolved separately to have different functions"
15:55:20 ClareS says "they may be in the same genome"
15:55:26 MichaelS says "For example human and bovine haemoglobin?"
15:55:41 VijayK says "http://bioinf.man.ac.uk/dbbrowser/bioactivity/thoeryc.html It should be right now"
15:55:42 ClareS says (to MichaelS) "yes, we are subdividing homologs"
15:55:47 CharafB says "..different alleles?"
15:56:07 ClareS says "human and bovine haemoglobin are orthologs"
15:56:23 IJT says "That's http://bioinf.man.ac.uk/dbbrowser/bioactivity/theoryc.html"
15:56:28 ClareS says "human haemoglobin and human myoglobin are paralogs"
15:56:42 ClareS says "does that make it clearer?"
15:57:18 RobertO says "so hence para=parallel evolution"
15:57:19 ClareS says "I think it would have been clearer if I had said "diverged" rather than "evolved separately""
15:57:29 MichaelS says "Sorry Clare, MUD time delays there! I'll need to work it out a second time."
15:58:44 ClareS says "Now, Charaf's databass question"
15:59:02 ClareS says "databass=database"
15:59:20 RobertO says "can you state then for me one more time, sorry the delay sometimes splits multiple comments"
15:59:43 ClareS says "there is not much difference between these databases, they are curated by different groups"
15:59:43 SarahL says " there sequence will be very similar and there function almost the same but there slight change in evolution gives the protein a slight advantage for that species"
16:01:27 ClareS says "many of these databases were developed before the Internet really took off, so different groups built similar groups in different formats and released them on CDROM"
16:02:21 ClareS says "even the two main DNA sequence databases, EMBL and GenBank were developed separately"
16:02:57 ClareS says "they contain the same data (apart from the most recent) but the file formats are slightly different"
16:04:13 CharafB says "Yes, we only have to submit new data once and they transmit to the other"
16:04:42 ClareS says "there will be a delay of a few days (!) while the data is transferred"
16:05:04 ClareS says "some fields in molecular biology aer moving fast enough for this to be important"
16:06:19 ClareS says (to LarryT) "by the way, thank you very much for posting your list of web sites to the list"
16:06:24 Glass says "I'm still 'listening' to you 'conversation' and I must say that I am impressed by the system. The transcript facility is obviosly very useful for going over past /recent MUDs."
16:07:36 VijayK says (to LarryT) "Thanks indeed! I was thrilled"
16:08:07 RobertO says (to LarryT) "yes thanks I may spend half a lifetime before I even scratch the links you provided. but I find having too much information better than not enough"
16:08:08 ClareS says "these sessions can be rather confusing with several conversations going on at once, and the transcripts help you make sense of them"
16:08:36 SarahL says "yes the transcripts are very good if you have missed a session or sometimes to clear up a point"
16:09:04 VijayK says "I archive all the transcritps"
16:09:22 ClareS says "I shall need to finish this session fairly soon, so are there any further questions?"
16:09:46 ClareS says "either bioinformatics questions, or questions to Robert?"
16:10:02 ClareS says (to Glass) "or questions *from* you to the students???"
16:10:10 VijayK says "Its a shame I was not ready with more on the topic. Hope to have another soon"
16:10:35 ClareS says "it was a little early in this topic for a MUD, but we couldn't alter the assessment schedule"
16:11:19 VijayK says "thank you it was just as well"
16:11:24 MichaelS says "Sorry, must go again."
16:11:24 RobertO says (to Glass) "have you spent much time moving around the course pages yourself and if so what is your opinion of the material and method, if I can be so bold to ask."
16:11:24 ClareS says "we will arrange at least one more session in the week beginning 21 Feb"
16:11:52 MichaelS disconnects.
16:11:52
LarryT PPS Telnet 1h 18m 1m 54s
MonikaS PPS HTTP 1h 20m 1m 3s
CharafB PPS HTTP 1h 20m 7m 39s
BartoszB PPS HTTP 20m 45s 20m 45s
ClareS PPS HTTP 1h 13m 28s
IJT PX HTTP 1h 17m 1m 17s
RobertO PPS HTTP 1h 17m 28s
VijayK PPS HTTP 45m 56s 33s
SpyrosS PPS HTTP 1h 6m 18m 48s
Glass PPS HTTP 26m 23s 8s
AttilaR PPS HTTP 42m 43s 33m 55s
SarahL PPS HTTP 34m 33s 3m 16s
16:12:15 VijayK says "Fine. Shall look forward to it"
16:12:50 Glass says "goodbye everybody. I have to go back to the team room. Good luck with the course."
16:12:54 ClareS says "I shall post the times to the discussion list as usual"
16:13:03 RobertO says (to ClareS) "if you have a mud that week could it be on tuesday, I will be at dartmouth college before that and at colorado state the days after, sorry for the special request"
16:13:50 CharafB says "Bye everybody, I must go too..."
16:13:55 Glass says (to RobertO) "Yes, I think the course looks very interesting. Goodbye."
16:13:55 CharafB disconnects.
16:13:55
LarryT PPS Telnet 1h 20m 3m 57s
MonikaS PPS HTTP 1h 22m 3m 6s
BartoszB PPS HTTP 22m 48s 22m 48s
ClareS PPS HTTP 1h 15m 1m 1s
IJT PX HTTP 1h 19m 3m 20s
RobertO PPS HTTP 1h 19m 52s
VijayK PPS HTTP 47m 59s 1m 40s
SpyrosS PPS HTTP 1h 8m 20m 51s
Glass PPS HTTP 28m 26s 0s
AttilaR PPS HTTP 44m 46s 35m 58s
SarahL PPS HTTP 36m 36s 5m 19s
16:14:00 ClareS says (to RobertO) "I will try but can't promise anything -- it couldn't be before 23:--GMT from what I remember of my schedule"
16:14:06 VijayK says "its my turn to say bye. I enjoyed the session. Thanks everybody"
16:14:21 ClareS obviously meant 23:00GMT
16:15:04 AttilaR says "I enjoyed it well, too."
16:15:15 SpyrosS says "Bye everyone, I have to go to ...."
16:15:19 RobertO says (to ClareS) "time isnt a problem it is just the day and I want to be able to participate more after I get a chance to work on this tutorial longer."
