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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.

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RobertO      PPS          HTTP    10m 12s   1m 20s
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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.
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RobertO      PPS          HTTP     11m 9s   2m 17s
MichaelS     PPS          HTTP     7m 30s      37s
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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.
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RobertO      PPS          HTTP    14m 12s   5m 20s
MichaelS     PPS          HTTP    10m 33s      19s
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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.
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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"
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15:17:19  Glass says "I can see why the web is great for a structural course - of course."
15:17:59  VijayK disconnects.
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RobertO      PPS          HTTP     23m 9s   3m 13s
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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.
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IJT          PPS          HTTP    26m 11s   2m 53s
RobertO      PPS          HTTP    25m 51s      53s
MichaelS     PPS          HTTP    22m 12s   2m 18s
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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.
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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.
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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.
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15:25:56  VijayK connects.
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IJT          PPS          HTTP    31m 26s    1m 4s
RobertO      PPS          HTTP     31m 6s       1s
MichaelS     PPS          HTTP         0s       0s
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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.
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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""
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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.
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RobertO      PPS          HTTP    42m 29s   1m 21s
MichaelS     PPS          HTTP    11m 23s   1m 40s
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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"
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MichaelS     PPS          HTTP    14m 22s   4m 39s
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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"
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RobertO      PPS          HTTP    47m 41s   4m 36s
MichaelS     PPS          HTTP    16m 35s   6m 52s
VijayK       PPS          HTTP    16m 35s   2m 44s
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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.
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15:45:29  Glass connects.
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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.
LarryT       PPS          Telnet   57m 7s  15m 43s
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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
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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.
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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
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Glass        PPS          HTTP     5m 38s   5m 38s
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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.
LarryT       PPS          Telnet   1h 18m   1m 54s
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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.
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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."