Mcb195-tf

mcb195-tf@lists.fas.harvard.edu

9 discussions

Start a nNew thread

Problem set 2 needs to be reposted...

by Jeremy Zucker

Hello Mike, The problem set that was posted is blank. Can you try reposting it? Jeremy

19 years, 2 months

Recitation locations?

by Jeremy Zucker

Hi guys, After waking up this morning, I realized that we don't have room numbers for the recitations in the syllabus. Do we know the locations, or does that still need to be decided? If someone does know, email me, and I'll put it on the website. Jeremy

19 years, 3 months

Re: [Mcb195-inst] Course website updates

by Jeremy Zucker

I sent this to the wrong address <mbc195-tf(a)lists.fas.harvard.edu> instead of <mcb195-tf(a)lists.fas.harvard.edu> the first time. On Wed, 2005-02-02 at 17:40 -0500, zucker wrote: > Hi Michael, > > Some confusion: > > The file called FirstOrder.m calls a function called FirstOrderODE > > The file called FirstOrderODE.m contains a function called FirstOrder. > > Shouldn't the function contained in FirstOrderODE.m be called FirstOrderODE? > > Sincerely, > > Jeremy > > Michael Springer wrote: > > >Looks good. > > > >A couple of minor changes. > >The first problems set on the assignment page has the wrong due date. > > > >Here are updated version of the matlab tutorial and problem set 1. > > > >Also here are two m-files that should be put in the matlab tutorial > >folder so people can download them. > > > >Thanks, > >Mike > > > >------------------------------------------------------------------------ > > > >function out = FirstOrder(t,input,param) > > > >%Constants > >kdecay=param(1); > > > >%Inputs > >A=input(1); > >B=input(2); > > > >%Differential Equations > >out(1,1)=-kdecay*A; > >out(2,1)=+kdecay*A; > > > >------------------------------------------------------------------------ > > > >%This is the file which will call up the ODE file to perform our numerical integration > > > >%Constants > >%param is our array of constants > >kdecay=1; > >param=[kdecay]; > > > >%initial values > >%Remember from our ODE file A need to be the first element of the array and B the %second element of the array. > >A=100; > >B=0; > >initvals=[A B]; > > > >%Accuracy of our integrate : Don't worry about this line. In fact you don't need to %include this; but you might want to use this some time down the road > >%1e-10 mean 1*10^-10 > > > >options=odeset('AbsTol', 1e-6, 'RelTol', 1e-6); > > > >%Set the Time length of the experiment > >%In this case the system will start at time zero and integrate to time 100 seconds > >tspan=[0 100]; > > > >%This next line is the meat and potatoes of the program. This line does calls our ODE file and does %the integration. There are several different types of numerical integrates. This is %beyond the scope of this class. > > > >[t x]=ode23t(@FirstOrderODE,tspan,initvals,options,param); > > > >%Watch your capitalization!!! > > > >%Graph the output > >figure; > >plot(t,x); > >xlabel('time') > >ylabel('Concentration') > >title('First Order Decay') > > > > > >

19 years, 3 months

Office hours...

by Jeremy Zucker

Hey guys, Send me times and places that you will have office hours and I'll put it on the web site. Sincerely, Jeremy

19 years, 3 months

Re: [Mcb195-tf] Re: Instructor toolkit access for MCB195

by Jeremy Zucker

Hi, A few more corrections and comments are listed below. Let's talk at 5pm about this. Where is Greg's lab, exactly? Jeremy On Tue, 2005-02-01 at 13:29 -0500, michael springer wrote: > Actually, can you post this version of the problem set. > > Thanks, > Mike >

19 years, 3 months

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

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

Mcb195-tf