Mcb195-tf January 2005

mcb195-tf@lists.fas.harvard.edu

2 participants
4 discussions

Randomness and Stochasticity in the Syllabus...

by zucker＠research.dfci.harvard.edu

Hello Becky, The syllabus you sent me takes an abrupt departure from the Gregorian calendar on March 10, 2005. I placed the corrected syllabus below at http://www.courses.fas.harvard.edu/~mcb195/lectures Sincerely, Jeremy Introduction Thursday, February 3 - In which we meet the mysterious prions and analyse their propensity for polymerization Marc Kirschner and Jeremy Gunawardena Dynamical-systems Tuesday 8 Feb - In which we encounter wild dynamical systems and explore their state spaces. Jeremy Gunawardena Linear-systems Thursday 10 Feb - In which we learn how to tame linear systems and determine their stabilities. Jeremy Gunawardena Oscillations Tuesday 15 Feb - In which we go round in circles. Jeremy Gunawardena Ultrasensitivity Thursday 17 Feb - In which we come to appreciate the virtues of sigmoidality. Jeremy Gunawardena Homeostasis Tuesday 22 Feb - In which we learn how best to remain equable in the face of adversity. Jeremy Gunawardena Molecular-circuits-I Thursday 24 Feb - The behavior of molecular circuits I. Dynamics of regulatory circuits in gene expression and development In which small molecules make big decisions. Walter Fontana Molecular-circuits-II Tuesday 1 March - The behavior of molecular circuits II. The topology of the possible: robustness, neutrality and evolvability In which we ponder on how evolution goes from here to there. Walter Fontana Networks-I Thursday 3 March - Networks: the properties of graphs In which we shall see that being connected is everything Walter Fontana Networks-II Tuesday 8 March - Network motifs and their significance In which math helps us to look at things we cannot look at. Walter Fontana Randomness Thursday 10 March - Randomness In which we toss a coin or two Walter Fontana Stochasticity Tuesday 15 March - Stochasticity in molecular decision processes In which we learn that nothing in life is certain Walter Fontana Searching-space-I Thursday 17 March - Searching space I. In which we consider how non-equilibrium dynamics gives polymers novel properties. Marc Kirschner Searching-space-II Tuesday 22 March - Searching space II The surprising similarities among the strategies used by ants, neurons and microtubules. Marc Kirschner Breaking-symmetry Thursday 24 March - In which we discuss how a homogeneous state can give rise to heterogeneity Marc Kirschner Spatial-patterning-I Tuesday 5 April - Spatial patterning I. Finding the middle, and further subdivisions. Marc Kirschner Spatial-patterning-II Thursday 7 April - Spatial patterning II. In which we consider the roles of induction and feedback in the development of robust patterns. Marc Kirschner The-role-of-evolution Tue 12 April - In which we discuss why things are the way they are. Marc Kirschner Bacterial-chemotaxis-I Thursday 14 April - In which we consider the problem faced by a small prokaryote in sensing a gradient, and learn how time helps. Lew Cantley Bacterial-chemotaxis-II Tuesday April 19 - In which the small prokaryote now faces a wide range of different concentration gradients: the role of adaptation. Lew Cantley Dictostelium-discoideum-chemotaxis-I Thursday 21 April - In which spatial and temporal sensing are invoked to explain eukaryotic directional motility. Lew Cantley Dictostelium-discoideum-chemotaxis-II Tuesday 26 April - In which we discover how spatial sensing is enhanced via feedback regulation. Lew Cantley Directional-motility-in-mammalian-cells Thursday 28 April - In which the mechanisms used by mammalian cells to achieve directional motility are elucidated. Lew Cantley Summary-of-motility Tuesday 3 May - In which all becomes clear, if not simple. Lew Cantley The-future-of-systems-biology Thursday 5 May - The future of systems biology. Marc Kirschner

19 years, 3 months

MCB 195 website URL

by zucker＠research.dfci.harvard.edu

http://www.courses.fas.harvard.edu/~mcb195 Administrative pages: http://www.courses.fas.harvard.edu/~mcb195/admin Right now, I am updating the website with the Lecture outline. I'm still waiting for Greg to send me the course syllabus and questionaire. jeremy

19 years, 3 months

Re: Instructor toolkit access for MCB195

by zucker＠research.dfci.harvard.edu

Hello Paul, Thanks for increasing the quotas. I have one more request: Could you give the following people administrative access to the MCB 195 course web site? Shai Shen-Orr <shenorr(a)mcb.harvard.edu> Mike Springer <michael_springer(a)hms.harvard.edu> Greg Lang <lang(a)fas.harvard.edu> There will be one more person, but I don't know his email address yet. Thank you, Jeremy > > > Dear Jeremy, > > We haven't forgotten about you. Since we're in the interim, we're > performing basic maintenance procedures on our systems to create more > disk space for everyone. The "M" accounts are being moved today and so > we can't bump the quota just yet. We hope to do so tomorrow. > > In the meantime, your email lists should be ready soon. > > Best, > > -- Paul > > On Jan 26, 2005, at 6:21 PM, Jeremy Zucker wrote: > >> Thank you for staying on top of this. >> >> I would like to set up mailing lists for the instructors and TFs. >> Please let me know as soon as the disk quota has been reset so that we >> can start adding content. The natives are getting restless. >> >> Jeremy >> >> On Wed, 2005-01-26 at 15:36 -0500, Phil Desenne wrote: >>> Dear Jeremy, >>> >>> We've placed a request for a 400MB quota increase for mcb195. We'll >>> let >>> you know as soon as it comes through. Videos are streamed from our >>> streaming video servers so the size of the video wouldn't affect the >>> course quota. If you would like more info regarding video and course >>> Web sites please contact icgvideo(a)fas.harvard.edu. >>> >>> Let us know if we can be of further assistance. >>> >>> Best, >>> >>> Phil >>> ----------------------------- >>> Philip A. Desenne >>> desenne(a)fas.harvard.edu >>> Senior Specialist for Instructional Computing >>> Instructional Computing Group >>> FAS Computer Services >>> Harvard University >>> >>> >>> On Jan 25, 2005, at 6:37 PM, Jeremy Zucker wrote: >>> >>>> Hi Gina, >>>> >>>> If last year used 145MB, I'd anticipate using at least that much, >>>> especially since we are planning to make the videos of each lecture >>>> available from our website. How much is an hour and a half of >>>> streaming video? If we don't have to host the video, then I'd still >>>> say 500MB to be safe. I'd hate to get to the end of the semester >>>> and find out we underestimated. >>>> >>>> >>>> Sincerely, >>>> >>>> Jeremy >>>> >>>> >>>> On Jan 25, 2005, at 4:45 PM, Gina Siesing wrote: >>>> >>>>> Aha! >>>>> >>>>> The problem is that the mcb195 account is over quota: >>>>> >>>>> Disk quotas for user mcb195 (uid 27948): >>>>> Filesystem blocks quota limit grace files quota >>>>> limit grace >>>>> /home17 146665* 100000 150000 none 88 10000 >>>>> 20000 >>>>> >>>>> Let us know how much space you anticipate needing for course >>>>> materials, and we'll request a quota increase from the FAS accounts >>>>> manager. >>>>> >>>>> You'll be able to add new folders and files as soon as the quota >>>>> for storage has been increased from its current 100MB limit. >>>>> >>>>> Best, >>>>> Gina >>>>> >>>>> On Jan 25, 2005, at 4:33 PM, Jeremy Zucker wrote: >>>>> >>>>>> Hi Gina, >>>>>> >>>>>> I went to Site Management -> Manage Tools & Folders, >>>>>> clicked on Add New Folder, >>>>>> In the text box in the pop-up form, I entered a name "test", then >>>>>> clicked Add Folder. >>>>>> >>>>>> Unfortunately, after performing these operations, the "test" >>>>>> folder did >>>>>> not appear in the Manage Tools & Folders page. Nor did it appear >>>>>> in >>>>>> the >>>>>> Student's View. >>>>>> >>>>>> Sincerely, >>>>>> >>>>>> Jeremy >>>>>> >>>>>> >>>>>> On Tue, 2005-01-25 at 16:26 -0500, Gina Siesing wrote: >>>>>>> Hi Jeremy, >>>>>>> >>>>>>> For adding new folders, you should just be able to click the "Add >>>>>>> New >>>>>>> Folder" link on the left side on the Site Management -> Manage >>>>>>> Tools & >>>>>>> Folders page. Do you see this link? You would give your new >>>>>>> folder a >>>>>>> name, and it should then appear on that Manage Tools & Folders >>>>>>> page >>>>>>> and >>>>>>> in the list of folders when you "Upload File/Image." >>>>>>> >>>>>>> If you already have a folder, but need to toggle from "hidden" to >>>>>>> "showing," you would click the blue link adjacent to the folder >>>>>>> name >>>>>>> under Manage Tools & Folders. >>>>>>> >>>>>>> Your HUID image should appear automatically if you click "Display >>>>>>> ID >>>>>>> Photo" under your name in the Teaching Staff tool. This is by far >>>>>>> the >>>>>>> simplest approach if you don't mind your ID photo as the >>>>>>> displayed image. >>>>>>> >>>>>>> Let me know if I'm not understanding the new folder question. >>>>>>> >>>>>>> Best, >>>>>>> Gina >>>>>>> >>>>>>> On Jan 25, 2005, at 4:21 PM, Jeremy Zucker wrote: >>>>>>> >>>>>>>> OK, I figured out how to get my image: >>>>>>>> http://www.huid.harvard.edu/faq/faq_images_capture.html >>>>>>>> >>>>>>>> However, we still can't work out how to add new folders. I'll >>>>>>>> swing by >>>>>>>> the Science Center tomorrow if I don't hear from you first. >>>>>>>> >>>>>>>> Sincerely, >>>>>>>> >>>>>>>> Jeremy >>>>>>>> >>>>>>>> >>>>>>>> On Tue, 2005-01-25 at 16:12 -0500, Jeremy Zucker wrote: >>>>>>>>> Thanks Gina, >>>>>>>>> >>>>>>>>> I have confirmed that I am now able to access the >>>>>>>>> Instructor's >>>>>>>>> Toolkit. One problem that Becky Ward noticed: Although I can >>>>>>>>> successfuly add web pages, I cannot seem to change the number >>>>>>>>> of folders >>>>>>>>> displayed. >>>>>>>>> >>>>>>>>> I have tried to do it through Manage Tools & Folders -> Add New >>>>>>>>> Folder - >>>>>>>>>> Add Folder >>>>>>>>> >>>>>>>>> I also tried to display new folders through Select Tools & >>>>>>>>> Folders -> >>>>>>>>> Submit Changes >>>>>>>>> >>>>>>>>> In both cases, there was no error message, but the changes did >>>>>>>>> not >>>>>>>>> take >>>>>>>>> effect. Finally, under Tools -> Teaching Staff, I tried to >>>>>>>>> add myself >>>>>>>>> (which succeeded), but I could not figure out how to upload an >>>>>>>>> image >>>>>>>>> of >>>>>>>>> myself. This will be important, because we have 4 instructors >>>>>>>>> and 4 >>>>>>>>> Teaching Fellows, in addition to the Executive Director (Becky >>>>>>>>> Ward) >>>>>>>>> and >>>>>>>>> the Curriculum Assistant (myself). We'll need photos just to >>>>>>>>> help our >>>>>>>>> students keep track of who is teaching them. >>>>>>>>> >>>>>>>>> Sincerely, >>>>>>>>> >>>>>>>>> Jeremy >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, 2005-01-25 at 15:00 -0500, Gina Siesing wrote: >>>>>>>>>> Dear Jeremy, >>>>>>>>>> >>>>>>>>>> You are now authorized for the MCB 195 course Toolkit. >>>>>>>>>> >>>>>>>>>> We're offering daily Toolkit workshops now through 2/4, in >>>>>>>>>> case this >>>>>>>>>> mode of orientation would be useful. The full workshop >>>>>>>>>> schedule is up >>>>>>>>>> on the ICG site at this address: >>>>>>>>>> http://icg.fas.harvard.edu/training/workshop.html >>>>>>>>>> >>>>>>>>>> All best, >>>>>>>>>> Gina >>>>>>>>>> >>>>>>>>>> On Jan 25, 2005, at 2:57 PM, Jeremy Zucker wrote: >>>>>>>>>> >>>>>>>>>>> Hello ICG folks, >>>>>>>>>>> >>>>>>>>>>> I am the curriculum assistant for MCB 195, and I will need >>>>>>>>>>> access >>>>>>>>>>> to >>>>>>>>>>> the Instructor toolkit so that I can familiarize myself with >>>>>>>>>>> the >>>>>>>>>>> system >>>>>>>>>>> and start publishing our course materials. Rebecca Ward >>>>>>>>>>> currently >>>>>>>>>>> has >>>>>>>>>>> access to the web site. However, she is out of town until >>>>>>>>>>> tomorrow. >>>>>>>>>>> >>>>>>>>>>> My Harvard ID is: 10631211 >>>>>>>>>>> >>>>>>>>>>> Please let me know if there is any additional information I >>>>>>>>>>> need to >>>>>>>>>>> provide you. >>>>>>>>>>> >>>>>>>>>>> Sincerely, >>>>>>>>>>> >>>>>>>>>>> Jeremy Zucker >>>>>>>>>>> Curriculum Assistant >>>>>>>>>>> Department of Systems Biology >>>>>>>>>>> Harvard Medical School >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> Dr. Gina M. Siesing >>>>>>>>>> Manager of Instructional Design and Development >>>>>>>>>> Instructional Computing Group http://icg.fas.harvard.edu/ >>>>>>>>>> Faculty of Arts and Sciences Computer Services >>>>>>>>>> Harvard University >>>>>>>>>> >>>>>>>>>> >>>>>>> Dr. Gina M. Siesing >>>>>>> Manager of Instructional Design and Development >>>>>>> Instructional Computing Group http://icg.fas.harvard.edu/ >>>>>>> Faculty of Arts and Sciences Computer Services >>>>>>> Harvard University >>>>>>> >>>>>>> >>>>> Dr. Gina M. Siesing >>>>> Manager of Instructional Design and Development >>>>> Instructional Computing Group http://icg.fas.harvard.edu/ >>>>> Faculty of Arts and Sciences Computer Services >>>>> Harvard University >>>>> >>>>> >>>> Jeremy Zucker >>>> Bioinformatics Specialist >>>> Dana-Farber Cancer Institute >>>> url: http://research.dfci.harvard.edu >>>> email: zucker(a)research.dfci.harvard.edu >>>> work: 617-632-6852 >>>> cell: 617-833-3196 >>>> >>> >>> > > > --------------------------------- > Paul F. Bergen > Senior Manager, The Instructional Computing Group > FAS Computer Services > Harvard University > ---------------------------------

19 years, 3 months

Harvard id's needed for website access...

by zucker＠research.dfci.harvard.edu

Hey folks, Just testing out the new mailing list. The quota has been raised, so I can start hacking on the web site. If you send me your Harvard id, I can set all of you up with admin access to the website. Greg, could you please add my name/email address as curriculum assistant to the syllabus? Also, could you send me an electronic version of the syllabus and survey so that I can post it to the website? Thanks, Jeremy

19 years, 3 months

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Mcb195-tf January 2005