• comments

• old business
  • gold line queueing
    • korve engineeering
    • MTA present * engineer from kentucky here * "reduced" 20-30 sec * trains gold line 190 weekday 164 weekend
      • 72 sec preemtion
      • 20 sec mandatory wait
      • electric train, doesn't have motion activated sensors? theyre fixed?
      • crossing appropach triggers activation process
      • to minimzie down times * first did the express service * change control system, allow higher speed * this allowed them to
      • 40 minutes down time... during track maintenance
      • broken down train, led to 5 minute down time
    • public comments
      • neil climan, resident association...
        • madison heights residents inconvenced.
          • queue lengs up to 600 ft, promised 40 -60 ft
          • streets are >85% of capacity, which means any error causes system to break.
          • Improvements to one direction hurts the other?
  • Professor Zimmer, CalPoly Pomona, Planner
    • Capstone, Studio class
    • Students present scope of work
    • results next march will be the students work

• History

  General Plan, Hisotry, Appleyard, Liveable Streets, 1981 www.trafficcalming.org neighborhood transportation managemant plan

  new zeland and australia have done some work trying to define environmental capacity.

  final deliverable an amend/supplement NTMP to define EC

  EC review would be trigered by NTMP, possibly...

• Plan

  • Literature Review, understand
  • Understand current NTMP process
  • Formulate Extensions
  • Street Classification
    • Minor, Major Arterieral, neighborhood street
  • Done by, May

• Street classification,

  Deemphasized streets, what is

• Todo,

  Read packet, Mobility Transportation Plan

  FHWA federal highway admistration map

• Public comments

  • Resident from south pas argued against the 710 tunnel. Oct 12

• Aproval of minutes

• council comments

  • I asked if the CCTV could be configured to trigger on bicycles on Lake and Del Mar.

• Staff updates

  • 710
  • bylaws
  • MTA Gold line issues brought the engineers from kentucky improved, by 20-30 sec. preemption signals have extend a marengo. MTA received kove report but hasn't really responded.

• Old Business

  • Ambassador West

    • Public Speak

      • RJ, CEQA issues?

        Points out that the harvest rock parking issues aren't really CEQA issues, they're a different type of problem. Argues not significant.

        • responds to harvest rock

          2,3,5,6,7 Argues that there are a number of parking lots nearby

      • Fred Zapeta, West Pasadeana Resident

        • does support the project, has some minor issues.
        • wants to minimize impact on orange grove, wants to put in Ts to prevent left turns on orange grove.

      • Serin ???, Kimbly Horn

        • Responsible for text portion of the mobility plan. Parking, confusion as term "Public Parking" but intended to be shared parking pg 18, 19

      • David Pool, Meranatha High school, President BoD

        • BoD supports the project.

        • Nature of joint use agreement.

          harvest rock, eclusive use of 293 parking, on saturdays & sunday doesn't have contratiual to 53 slots, but plan on continuing. can coordinate to share parking for use on other times

    • Doug Hues, Dir Oper, from HR

      The list they provided was "history" for WCG, they concerned about maintaining access for concert events

    • Steve Ross, Dir Planning ? Homes
      • mentions what pasadenas zoning code, 1262 seats, need 1 car per 5 seats? 252 spaces
    • Greg ? Applicant
      • Pg 4 of harvest letter, paragraph A, 2nd paragraph want to have rights "running with the land" not owner. they didn't, but they didn't negotiate for those rights.

• Commissioners, questions

  • the applicant thought WPRA's suggestion for a t-bone curb was a good idea

  • Chair, says there may be too much parking for the sunrise use. parking for sunrise will be determined by the CUP process

  • Route for certification for this proejct,Daryl ? from Planning Commisison

    Parts will go through planning, but the fina EIR goes to councila

    Chair, recommends that their be more consistancy in how EIRs are reviewed.

    person from city legal, describes that the process is more orderly than it appears. requires certification before discretionary action

• Send comments to Chair and Vice Chair Juan Velasquez, Vince Farhat who will summarize

• Close of public comments * oral, Oct 11, written, Oct 30
• Pedestrain Saftey vide
  • given out 500 bike helmets
• Pedestrian Committee, Comissioner Delgado
  • Showed a group of students for a community planning class, cal poly, pomona always use a real client, students develop scope of services

• Call to order

• Roll Call

  • Vince Farhat
  • Diane Trout
  • Jennifer Higginbotham

• Public comment

• Commissioner Comments

  • Asks about distribution of and update of bike master plan
  • chair, discussed westage sept 18th, before council
  • for ambassodor west, try to have comments ready (in writing) for next meeting.

• Approval of minutes

• Staff activities

  • Eric Chen, $450,000 for construction of bicycle boulevard project
    • finishing paperwork
    • north marengo between orange grove and washington

• Old business

  • trip rededuction (transportation management plan) recommend 75,000 sqft.
  • Gold line queuing
    • short term
    • korve was initial engineering review firm for the gold line
    • peer review, doesn't have detailed knowledge of system
    • "abnormal number of atypical events"
    • reverse coordination, free the front of a queue, instead of typical moving wave of green
    • sometimes hold the train to let the traffic clear, especially when at stations.
    • the flashing yellow, is to avoid the "yellow" trap, supposidly not to confuse drivers
    • longerterm
      • try to make meets very clean at california
  • there's a required study for the flashing yellow

• Caltech Master Plan

• Ambassador West

  • oct 11 public meeting
  • harvest rock church, pastor
    • started recently
    • parking serious problem
    • conference world wide
    • are responsible for running ambassador auditorium
      • want to state mission...
    • wants public parking in the area.
  • doug huse, manager
    • about 600 cars
    • 10 parking "clusters"
    • multiple owners of the facility
      • only 3 clusters on the campus still available.
      • EIR, removing 140 parking spaces...

  • 2008 40 events?

  • Charles Kenny,
    • wants to know what the 30 spaces are for?
  • clarification
    • one report by applicant, one by consultant.
  • Does SEQUA require that negative parking impacts be addressed?
    • unclear, very techincal law question

• send comments to bauman

• AutoLigand AutoDock, Rodney Harris

  • Tool for "rational" ligand design
  • computes affinity

• GpuPy, Benjamin Eitzen, WashU

  • strengths
    • currently improving faster than traditional cpus
  • weaknesses
    • single precision
    • data must be copied to gpu
  • programmability
    • newer gpus can execute programs in "high level" languages Cg GLSL HLSL
    • programs are called shaders
  • how it works
    • GPU executes program once for each pixel that is drawn to screen
    • overrrides default numpy functions, can be transparent
    • some functions are slower on gpu (like simple add or multiply)
    • some get faster with larger N (pow, arccosh)
    • some are just faster (cos, sin)
    • the more complex you can pass over the faster, correlation
    • not hooked up yet, but have edge detection filter
  • possible future work,
    • autoconfig
  • simulation of double with singles hal.ccssd.cnrs.fr/ccsd-00021443
  • htpp://eecs.wsu.edu/~eitzenb/gpupy

• Boost Graph Library, Douglas Gregor

  • path finding

  • connectivity & clustering

  • network flow

  • coloring

  • layout & visualization

  • motivation

    • python is easier to teach
    • dynamic features of python
    • usabiliy (e.g. c++ error messages)

  • Task: network tolerance

    from boost.graph import * g = read_graphviz("network.dot")

    bicomponent = g.add_edge_property(name='label', type='integer) art_points = biconnected_components(g, bicomponent)

    for v in g.vertices:

    if v in art_points:

  • graph types in python

    • Graph
    • Digraph
    • Graph exploration interface

  • vertex and edge properties

    • attach additional model domain knowledge
      • computer net, vertex(host, ip_addr), edge(bandwidth, latency)

  • Properties in the BGL

    • property map
      • implicity, just access property
      • explicity, allows more specifity, 2 params optional weight = g.add_edge_property(name='weight', type='float')
    • using property maps
      • similar to dictionaries (weight[e], =0.75
      • pass to algorithms dijkstra_shortest_path(g, start_vertex, weight)
    • has visitor model to do something when you hit interesting points in the algorithm. (e.g. debugging, new algorithms)

  • http://www.generic-programming.org/~dgregor/bgl-python/

• summary of research issues with/Fast multipole Algorithm, Idesbald van den Bosch

  • ship signature reduction
  • lots of details about problem and need for optimization
  • gmsh (mesh generation)

• Object Oriented Finite Elements, Andrew Reid

  • OOF2,
    • rapid construction of meshes adapted to irregular microstructural geometriesp

• Parallel PDE solvers in python, Bill Spotz

  • trilinos project
    • provide central repository for sandia's solver
    • http://softwrae.sandia.gov/trilinos

• Python imaging tools for reconstructing magnetic resonance images, make trumpis

  • https://cirl.berkeley.edu/view/BIC/ImagingTools

• PyRoot, Wim Lavrijsen (pronounced more like vim)

  • http://cern.ch/wlav/pyroot/
  • ROOT root.cern.ch
  • reflection for C++ (reflex, http://cern.ch/seal-reflex)
  • they combine reflection based meta-information to generate python wrappers on the fly.
  • also can call python from C++/CINT
  • very impressive looking

• QScimpl, Eric Dobbs

  • personal, dobbse.net
  • Tech-X Corporation, txcorp (scientific physics stuff)
  • mostly decided to advertise the advantage of simplicity

• Genesis SciFlo, Scientific Knowledge Creation on the Grid, Brian Wilson

  • Problem, terabytes of data (years) distributed at several data centers
  • iEarth
  • showed an updating svg diagram showing the execution of their workflow.
    • distributed across many machines via web services
  • data access protocol, retrieve chunks of data over web.
  • used xpath to extract results from amazon soap results
  • software shipped
    • lxml (XPath 1.0)
    • twisted, pyldap, openldap,
    • sleepycat dblxml has xquery and xpath
    • dojo AJAX library
    • openDAP, extract cdf, hdf file
    • globas v4 grid
  • globus v4 is supposed to be soap webservice
  • WSRF (web services resource framework)
  • UDDI universal description discovery and integration, find service
  • grid workflow,
  • rest vs soap, each have advantages/disadvantages
  • UDDI4py from IBM, SOAPpy
  • recommends more XML microformats for "mash ups"
  • publish science algorithms as reusable web services
  • www.opendap.org

• Python Web & Grid Service Tools, Keith R Jackson

  • Globus toolkit
  • decided to simplify system by standardized into webservices
  • helps organize coordinated usage of resources
  • his mac crashed
  • SOAPpy is officially unsported
  • ZSI is hopefully the "new" better way, though they're more complicated than SOAPpy
  • XML schema scary complicated
  • Mapping tool from WSDL to python (wsdl2py)
  • using m2crypto (they thought it was being supported, unlike pySSL)
  • LIGO used it to ship 50 terabytes of data through pyglobus
  • WSRF supposed to define way to hand stateful connections
  • lifecycle, things will die at some point, though can be refreshed.
  • WS-N another webservices spec
  • seems to actually work, java, C, python call all talk.
  • PyCLST
  • GridFTP, implement extra features to handle transfer over highperformance network
  • Visual programming environment, useful for viewing workflow
  • Userinterface
  • planner, condor, dagman
  • exec manager (CBEI)
  • exec context
  • physical resources
  • pyGlobus, http://dsd.lbl.gov/gtg/projects/pyGlobus/
  • ZSI, http://pywebsvcs.sourceforge.net/zsi.html
  • pyGridWare, http://dsd.lbl.gov/gtg/projects/pyGridWare
  • ViCE, http://dsd.lbl.gov/gtg/projects/vice/
  • PythonCLServiceTool, http://dsd.lbl.gov/gtg/projects/PythonCLServiceTrool
  • everything BSD license
  • eclipse has a nice WSDL interface generator
  • python to wsdl would require static type annotation.
  • webservices, text to do control, then binary for shipping data
  • amazon, uses a very efficient xml binary encoding

• Seeing through the MIST, Tripp Lilley

  • interesting point about maliable UIs
    • how do you let a user, know theyre changing their world, and revert.
  • super early project, not even screenshots

• They'll video tape

• Cancelations, so some one could move to tomorrow

• Python3, Guido's Talk

  • Python 2.5, some improvements

  • Python 3000

    • Language update
    • Stroustroup compatibility
      • C++ backwords, add a new keyword, was a major incompatibility
    • Perl 6 other extreme

  • -Q warn about integer errors, // <- integer division

  • Pep 3100 for info, python.org/dev/peps

  • guidos blog, artima.com/weblogs/

  • big changes

    • kill classic classes
    • Exception derive from single root
    • absolute import ( can be turned on in 2.5 )
    • replacement for d.has_key if x in d
    • interating over file is better than xreadlines

  • smaller changes

    • exec, function again

    • x in favor repr(x)

    • except x,y,z as err instead except e,err

    • generator replaces list comprehension * list comprensions currently leak their name into the surrounding

      System Message: ERROR/3 (<string>, line 38)

      Unexpected indentation.

      scope

    • kill raise E, use raise E(arg) (work away from string exception)

    • xrange has a problem with long ints

      • will change range to do xrange things with lon support

  • string type updates

    • string becomes unicode
    • also introduce a byte type, all conversions from byte to strings require specifying conversion

  • new standard i/o stack

    • replace the c stdio with something a bit more inspired by java * unbuffered io * buffered io built on top
    • see sandbox/sio/sio.py for early prototype

  • print becomes a function

    • easier to change print to something
    • 2.x/3 compatibility requires only printing single string

  • dict views instead of lists

  • drop default <, <=, >, >= for classes (currently does memory)

  • Google python sprint next week

• Understanding NumPy, Travis Oliphant

  • numeric compatibility layer, numpy.oldnumeric
  • dtype object ( defines what the elements of the NumPy array )
    • array scalar ( wraps element returned from cell )
    • dtype code '<i4' (byte order, type, size)
    • isbuiltin, 21 static objects
    • dt.itemsize
    • fields, since array is just chunks of memory, because of alignment issues
    • a.flags ( properties on arrays )
    • a.empty((10,),dtype='int,float,a10') * a.dtype * a.dtype.fields
    • arbitrary structure needed to memmap complicated files

• Extending NumPy, swig, f2py, pyrex, ctypes,

  • swig, first
  • weave, embed C code in python string, kinda fortran like in variable names
    • compiles on the fly
  • pyrex
    • from c_numpy cimport, ... import_array()
  • ctype, calls shared libraries
    • .argtypes allow specifying type checking for c calls

• Python for modern scientific algorithm development, Fernando Perez

• Building a Distributed Component Framework (pyre), Michael Aivazis

  • distributing apps on many machines is hard
  • user space, ssh, scp, pyre services
  • pyGridWare (Kieth jackson)
  • gsl
  • http://www.cacr.caltech.edu/projects/pyre
  • http://pyre.caltech.edu (soon)
  • relase early 2007

• Enthought tool suite

  • What are traits?
    • notification (considered important)
    • visualization

• Synthetic Programming with Python

  • provide low level access to cpu without doing string processing
  • http://www.synthetic-programming.org

• 3D visualization with TVTK and MayaVi2, Prabhu Ramachandran

  • Traited VTK
  • MayaVi2 uses enthought exposes lots of objects and gui tools for playing with them

• Realtime Computing with Python, Andrew Straw

  • introduction to relatime simulation of fly
  • http://dickinson.caltech.edu/Research/Grand_Unified_Fly
  • comedi control measurement device interface

• Lightening Talks

  • Dude from JPL, Mike Ressler
  • Future of IPython, Brian Granger, Tech-X corp
    • planning on extending to ipython to do distributed programming
    • control remote supercomputers from laptop
    • support multiple parallel types
    • focus on interactive work
    • distributed programming in python
      • multiple processes, threads are limited by GIL
      • non-blocking sockets
      • asynchronous error/fault
  • Travis Oliphant, about PEP
    • using trac pages for NumPy http://projects.scipy.org/scipy/numpy
    • table @ dinner about arrays
  • Travis Vaught, Enstaller
    • egg package installation manger
    • has post-install scripts
    • build egg from pointing to a directory
    • code.enthought.com/enthon/enstaller.shtml
    • enthought.com/enthought/wiki/Enstaller
  • The Current State of Vision, Michel Sanner
    • Visual programming tools
    • supports nested graph nodes
    • looks written in tk
    • www.scripts.edu/~sanner/software
  • Quick overview of Chaco, Peter Wang
    • chaco visualization tool
    • http://code.enthought.com/chacho

• SAGE, Alex Clemesha

  • good environment for algebra, number theory, geometry
  • what is it
    • Distribution of math software
    • python library
    • new interface to math software
  • where is it: modular.math.washington.edu/sage
  • their ajax based web notebook looks really impressive

• Mathematica like plotting for SAGE, Alex Clemesha

• BioHub, Diane Trout

• Software Carpentry, Greg Wilson

  • he's a good speaker.
  • debugger for make
  • debugger than can trace back and forth between python & c code
  • Guido pronounced django the web framework.

Mapping Gene Regulatiry Networks in Yeast using DNA Microarrays, proteomics

and genmapp.

Oitvai Barabasi 2002 neat graphic showing different levels of cell organization.

cold shock (because it's illstudied so far)

GenMAPP, draw pathway, color

www.genmapp.org

cold shock (because it's illstudied so far)

• covering the 3 things that changed since their last meeting

Whats "sequa"

• there's already some conditioning of a project build, how does this fee extend things.
  • How are the funds going to be spent?
  • Does it help with streamling other aspects of the project
• The fee goes away when the projects finish
• The fee is attached to building those $54e6 of projects.
• they want some more detail about how it'll help, save some of the discussion.
• doesn't it set a bound on how far the the developers study has to extend.
• they want a industry specific FAQ
• is there a way of more specifically planning out what improvents are needed so the developers can have less uncertainty about a council or developer suddenly want something new.
• Arts busses need to be frequent reliable convient
• Would it be possible to opt in?
• May 5th tac meeting 7.30 am

sometime ago my laptop and phone were paired, but at some point I

deleted one of the connections, and when I tried dialing out the phone wanted a passphrase and kde thought there already was one.

I tried to delete /etc/bluetooth/link_key but that didn't work. Eventually I changed the pin-helper in hcid.conf from the kde one back to the bluez one.

I they started a connection and rand the pin-helper manually. One copy of the helper started up, and then magically another one popped up. I then filled a pin into both the second pin-helper and my phone and was able to make an outbound connection.

Of course then my ppp settings were wrong.

I commented out any fixed address, and the dns server information, and then used the /etc/chatscripts/provider which was setup to dialout to *99***2# (the second dialup profile on my phone)

System Message: WARNING/2 (<string>, line 16); backlink

Inline emphasis start-string without end-string.

I also added

iface ppp0 inet ppp

provider p900-blue

to my /etc/network/interfaces but i don't think that was important in this case.

And now, once again I can connect to tmobile via my phone

I need to make sure i keep my phone better charged.

I wanted to make sure that I can build Qt apps on os x, the documentation is a little bit weak, especially with respect to explaing how to get qmake to automatically shove the right framework components into the .app bundle.

However the following steps were able to build an appropriate bundle.

export QTDIR=/usr/local/Trolltech/Qt-4.1.0 export APP=hello mkdir ${APP}/Contents/Frameworks rsync -av --exclude "_debug" --exclude "Headers" ${QTDIR}/lib/QtCore.framework ${APP}.app/Contents/Frameworks rsync -av --exclude "_debug" --exclude "Headers" ${QTDIR}/lib/QtGui.framework ${APP}.app/Contents/Frameworks rsync -av --exclude "_debug" --exclude "Headers" ${QTDIR}/lib/QtOpenGL.framework ${APP}.app/Contents/Frameworks

install_name_tool -id @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore ${APP}.app/Contents/Frameworks/QtCore.framework/Versions/4.0/QtCore install_name_tool -id @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui ${APP}.app/Contents/Frameworks/QtGui.framework/Versions/4.0/QtGui install_name_tool -id @executable_path/../Frameworks/QtOpenGL.framework/Versions/4.0/QtOpenGL ${APP}.app/Contents/Frameworks/QtOpenGL.framework/Versions/4.0/QtOpenGL

install_name_tool -change ${QTDIR}/lib/QtCore.framework/Versions/4.0/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore ${APP}.app/Contents/MacOS/${APP} install_name_tool -change ${QTDIR}/lib/QtCore.framework/Versions/4.0/QtGui @executable_path/../Frameworks/QtGui.framework/Versions/4.0/QtGui ${APP}.app/Contents/MacOS/${APP} install_name_tool -change ${QTDIR}/lib/QtCore.framework/Versions/4.0/QtOpenGL @executable_path/../Frameworks/QtOpenGL.framework/Versions/4.0/QtOpenGL ${APP}.app/Contents/MacOS/${APP}

install_name_tool -change ${QTDIR}/lib/QtCore.framework/Versions/4.0/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore ${APP}.app/Contents/Frameworks/QtGui.framework/Versions/4.0/QtGui install_name_tool -change ${QTDIR}/lib/QtCore.framework/Versions/4.0/QtCore @executable_path/../Frameworks/QtCore.framework/Versions/4.0/QtCore ${APP}.app/Contents/Frameworks/QtOpenGL.framework/Versions/4.0/QtOpenGL

There's probably some way of emedding that in a .pro file, but I don't know it yet. Also the cp -R really should be modified to not copy the header and debug parts of the framework if one wants a reasonable download size.

• adjustments to to the agenda
  • note that they only did the automobile counts?
  • the comment about "report card" measurements
  • fuller EIR,
• Los Angeles Times
  • changes in suburban development, complimentary to pasadena
• Floraline Stevenes, PhD, Educator, new comissioner
• Roger suggests that the commussion form a working group, on bike parking. Gray, DelGado, Valesques
  • Zoning code is online
  • Urban land institute, shared parking analysis, residental parking for apartments & condos, 1.5, 1.7 dwelling units
  • Survey of 4000 urban california parking 1.59 parking spaces per unit.
• Trip reduction ordance
  • is there data available of how many properties meet these various thresholds
  • They need to determine the remaining fee structure
  • talk to city attorney
• Westgate Draft EIR
  • Apeals, 10 days after action item
  • Last day pubic coment feb 21st
  • Public comments
    • West pasadena resident association
    • has many issues with EIR
    • substitution of max for minimum for
    • changed intersection policy from D to E (long lines, waiting through several cycles)
  • there's a computer model of the traffic plan Wonder if one can get it?
  • Comissioner comments
    • Roger points out the lack of pedestrian data
    • comissioner delgado , why aren't there more counts
      • 2015, allows minimum requirement traffic E
  • next comissioner
    • why isn't there more commercial
    • 10' setback from street isn't walkable
    • several intersections drop to E or worse, is that to encourage mass transit by preventing anything else from working
• Planning commission
  • Feb 22

need multiple screenshots of larger myogenen pathway

need multiple genomes, cistamatic might have some

dog, mouse, human, opossum, chicken, fish, fugo,

old mouse genome, had some issues

worry about holes in the genome, can cause drops of regions?

whats a core genome? is it quality of genome, or is it evolutionary distance?

go down to next gene go up 50 kb/then overlapping modules including the next/

• Call meeting to order

• Public Comment
  • Previous secretary said thanks
• Agenda Updates
• Commissioner Comments
  • Sir Peter Hall, Address, nifty ideas about transit
  • There was an interruption on the gold line, MTA responded, There was questions about what the MTA did for the rose parade
    • MTA managers at stations to respond the accident, quickly set up bus bridge
  • They're going to be quite busy for the next 6 months, number of big projects.
• Westgate , Robert ?, vincent gonzeles, Draft EIR
  • Green/Delacy/Del Mar/Pasadena, 11.94 acres
  • 820 residental units
  • comment period ends feburary
  • Impacts (Minor)
    • there are underground storage tanks which need to be evaluated for being closed and for whats in them
  • Imapacts (Significant)
    • Air Quality, construction, operation,
    • Public Services, multiple projects are going to put a drain on police & fire
    • Traffic, construction of this project, and others in the same area increased vehicle trips
  • Traffic (Traditional)
    • evaluated to 2015 using models from the general plan
    • Yay metioned bike parking (according to bike plan)
    • trip reduction plan according to city trip reduction ordanence
  • Comissionars comments, review EIR, bring comments in writing
    • is the staff going to bring the report back to TAC
    • roger wants to see the Pedestrian and bike data because its in transit zone? They don't have it.
    • Carolyn Naber, Annual report card, evaluate how well mitigation measures work
      • record scoping standards
      • project travel times needs to be done, but doesn't necessarily need to be in the EIR
      • discussion
      • why the consultant didn't come up with clever things for net zero traffic increase
        • Arts system contributions?
        • Page 60 of traffic study
        • project is going to contribute to nexus project 50-60% to transit
        • Lake zone has plans to offer residents passes for 1st year
• Fuller EIR
  • 60 day review Feb 21st
  • corsen to union/ madison el molino
  • 857 Units add to campus walnut /corsen
  • more academic space
  • 500 space parking strucure walnet/madison
  • mitigation
    • traffic camera
    • extend traffic links
    • expand fullers road share program
    • some bike parking spaces, improved bicycle racks
    • installation of a 1 countdown traffic signal
  • comments,
    • perhaps flex car system for students
      • variance because of a city traffic ordances
    • commisionar impressed with
      • pedestrian corridor
      • 1.5 persons per car trip (aparantly very high)
• My general Questions?
  • anyone done trip surveys of various pasadena resients? personal trip logs?
  • what about trying to get in the pay as you go car insurance programs
  • Whats ITS program

I got talked into darcs and now want to be able to check out my patches on

my nslu2. Unfortunately darcs requires ghc, and ghc requires itself to compile. This leads us to the joy of making a new port.

http://www.haskell.org/ghc/docs/latest/html/building/sec-porting-ghc.html

I started with the above link and tried to get it to work. So far, the files they tell you to copy includes/(ghcautoconf.h DeriviedConstants.h GHCConstants.h) are not created by the configure step so you need to run make boot in the ghc directory on the target.

Then after copying them over make them read only, as my touches weren't enough to prevent their makefiles from trying to rebuild those files.

i managed to get it to start building, but it died trying to make the compiler with a bunch of cast errors.

I've been trying to setup a VoIP system at home ('cause) and can call

my cordless phone (plugged into a SPA-3000) from a IP Phone (grandstream gxp-2000)

That's all good and works fine. I then decided to go further and plug the SPA-3000's FXO(?) port into my vonage ATA. I can get it to make outgoing calls, and sometimes even incoming calls.

I can't get authentication to work for outgoing, and I can't get caller id to work for incoming.

This thread was rather helpfull on getting the calls working.

..:

[spa_outbound] type=peer secret=<SECRET> port=5061 host=dynamic canreinvite=no nat=no qualify=yes dtmfmod=rfc2833 context=incoming-vonage

is my current outgoing config.

On the SPA I have the PSTN line registering seperately from the ATA line.

If I want to get things to autoforward to the server I need to set PSTN Ring Thru Line 1 to off and to set a dial plan to SO< s:@server.host:5060 > (And of course tell the PSTN which dial plan to use.)

If I set the CID on, asterisk 1.2.1 gets very confused about the source SIP address and chokes. I tried setting things to insecure=very but to no avail.

I'm thinking I might try openser, as its more sip orientated. (Though there documentation is quite sparse).

I found some documentation on the SPA-3000

Eric showed up to advertise his stochastic grammer techonology. http://computableplant.ics.uci.edu/papers/StochProcSemanticsTR.pdf

It appears to be a production rule -> result with a probablity Of course the various components can be mutualy dependent on various state parameters.

The question is can this be used for biological network evolution?

E.g. simplified cell cycle?

Also Eric's papers are linked from http://www.ics.uci.edu/~emj/

I've been digging through ~kent/src looking to see how the UCSC browser works, so we can write our own API for grabbing data out of it.

Table descriptions from from .as files (autoSql) and are loaded into tableDescriptions.

There's grp table which lists the defined groups.

The map between tables and which group they belong to appears to come from *.ra files. I haven't found a place in the database where they're stored yet.

System Message: WARNING/2 (<string>, line 10); backlink

Inline emphasis start-string without end-string.

We're trying to determine if there are repeats near genomic probems.

The first pass file had a large number of repeats in it.

high_genomic_signal_fewer_repeats.txt had those stripped out.

I created a fasta file with the following python code

data = [ x.strip().split('\t') for x in open('high_genomic_signal_fewer_repeats.txt','r')]
open('high_genomic_signal_fewer_repeats.fa','w').writelines([ ">%s|%s\n%s\n" % (x[2],x[0],x[3]) for x in data])

ok yeah I shouldn't do that in so few lines.

Hopefully the following

blastall -p blastn -e 0.000001 -d mouse_34.0.fa -i high_genomic_signal_fewer_repeats.fa -m 7 | tee high_genomic_signal_fewer_repeats.blast.xml

command will generate a new, smaller xml results file.

I've wanted to try to use python & boost for a while, but their tutorial depends on using bjam, which has been a pain to try and figure out. And of course the boost-python developers think that jam is the best thing ever and don't bother providing any documentation of how to use boost-python in a more traditional environment.

Here's my stab.

/* hello.cxx */
#include <boost/python.hpp>
using namespace boost::python;

char const* greet()
{
  return "hello, world";
}

BOOST_PYTHON_MODULE(hello)
{
  def("greet", greet);
}

I compiled it on an amd64 linux box with the following.

$ g++ -c -fpic -I/usr/include/python2.3 hello.cxx -o hello.o
$ g++ -shared -fpic -lpython2.3 -lboost_python hello.o -o hello.so
$ python
>>> import hello
>>> print hello.greet()

It turns out the -fpic is required for the AMD64 box, and on an x86 box, is unnecessary. (Though it doesn't hurt to have leave it in).

Would it have been too hard to show the manual way before extolling the virtues of their build system? Perhaps they were just being lazy as coming up with a simple build script on windows would probably be a lot harder than the above.

I was looking at the log files and discovered that pidentd was throwing error messages about netlink_lookup: write failed: Connection refused

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=305926

Seems to suggest that adding the module should make it shut up.

So I added the following to /etc/modules # tcp_diag may shut pidentd up about netlink_lookup: write failed tcp_diag

• practical "blunts" cassi?
• what was the name of the guy who made the really good wasters.
• balance was only an inch or two above the hilt, the pommel was much narrower than mine. beautifully smoothed.
  • should take picture of it before leaving.

• Subversion

  The full documentation for subversion can be found at http://svnbook.red-bean.com/ However here's a quick introduction.

  Subversion is a version control system designed to fix several issues that were found in cvs, such as being able to rename files and process binary files more efficiently.

  Version control systems allow one to keep track of how a file changes over time, and help multiple people who are modifying the same file. For instance if two people had copies of a file and each independently added some text, if they wanted to merge the file one of them would have to take the others file and attempt to identify the differences and merge the two together.

  Subversion, however, would attempt to merge the two chunks automatically. It does this by seeing if the changes touch the same line of text, if they do it will generate a conflict, otherwise it will go ahead and merge them.

  It will also help you roll back to a previous change, or compare how a file has changed over the past few months.

• Subversion Quick Start

  svn co <svn url> [destination] (checks out a subversion url to either the name of the last part of the url or the optional destination name).

  svn update when run in a project directory will update to the latest version of that project.

  svn status will show you what changes you've made to the directory try

  svn status -u will check the network to see if there are an updates

  svn commit [filename filename ...] will commit either everything (when there are no files, or the specific file list to the archive)

• OS X Subversion

  Command line copy of subversion built for OS X is available at http://metissian.com/projects/macosx/subversion/ or http://www.codingmonkeys.de/mbo/

  Documentation on installing a Mac OS X subversion client is availabe at

  http://weblogs.uncc.edu/blog/jwedgeco/2004/08/17/mac_os_x_subversion_client_works

to 877-771-0077

idle measurements base 20 watts Via C3 no cards, 44 Amd64 pci-x, 78

Filled out 09/27/2005 at 23:58:38 Auth # 028920

• asked about biohub
• show list of orthologs
• links to expression array
• links to motifs
• link to structure
• show data source
• map viewer

So I read through quite a bit of the samba howto and finally got samba setup.

One big problem I ran into was the following

operation is not possible without initialized secure memory (you may have used the wrong program for this task) [2005/08/16 14:24:27, 0] smbd/server.c:main(798)

It appears that happens when I have SSL or TLS initialized, I solved it by upgrading libldap2 from 2.1.23-1 to 2.1.30-8 and libgnutls7 from 0.8.12-3.1 to 0.8.12-7

• Getting ldap auth working

apt-get install libnss-ldap pam-ldap

Still have some big problems in that i have too many different password databases floating around.

I tried getting chilispot working, but it needed to talk to my webserver/radius server which is the main thing i'm trying to protect. Since I also didn't feel like getting radius properly setup, I just punted and went for the simpler WPA-PSK configuration.

However before I went simple I split the wired and wireless networks into two IP address ranges, and I renumbered my IP address space out of 192.168.1

I followed wiki.openwrt.org/HotspotOpenvpnHowto to split the wifi (many nvram commands) Later I discovered that some of my problems getting chillispot working were actually caused by routing issues so I needed to add iptables -A FORWARD -i eth1 -o vlan1 -j ACCEPT # wifi to outside iptables -A FORWARD -i eth1 -o vlan0 -j ACCEPT # wifi to lan iptables -A FORWARD -i vlan0 -o eth1 -j ACCEPT # lan to wifi

I also added slightly more generalized commands to the firewall.user

Eventually I decided I didn't actually need the complexity of chillispot yet, and just started down the WPA-PSK path

http://openwrt.org/OpenWrtDocs/nas Gave some information on setting up the propritary wpa config tool.

I also installed wpasupplicant on my linux laptop. Theoretically it'd be better if I actually got the WPA2/cert mode working, but eh, i'm not ready for that yet.

To get wpa working on the WRT54G I needed to add

nvram set wl0_akm=psk nvram set wl0_crypto=aes+tkip nvram_wpa_psk=<password>

I needed both wl0_akm and wl0_crypto for openwrts nas startup script.

Next I need to move the mini out to the living room, and then set up a some kind of client box in my office. Do I try for getting LDAP authentication working so I can unify the passwords between my mac, my windows partition and all my linux boxen?

$ ldapsearch -H ldaps://127.0.0.1/ -b dc=mydomain -x ldap_bind: Can't contact LDAP server (-1)

It turns out that the problem was in my /etc/ldap.conf file

http://www.openldap.org/lists/openldap-software/200409/msg00060.html

suggested using -d 1

The interesting line was

TLS: could not load verify locations (file:/etc/ldap/slapd.pem',dir:').

Ah! I'd renamed that file... so it was trying to validate the self signed server cert which wasn't working... ok

However the openldap howto http://www.openldap.org/pub/ksoper/OpenLDAP_TLS_howto.html recommended putting both the public and private key into the same file. Since it appears i need to distribute the key to my client machines it'd be really nice if they were seperate.

Ok now I get it...

In the ldap.conf file you need to make sure that TLS_CACERT is pointing to either the certificate (for self signed certs) or the certificate authority chain (for trusted certs)

Note it's also important for the base to be set properly in /etc/ldap/ldap.conf (it certainly cuts down on the amount of typing one needs to do)

To get apache to work I needed to add LDAPTrustedCA /etc/ldap/mus-slapd.crt.pem LDAPTrustedCAType BASE64_FILE to get apache to me happy with my cert, and i still think its using ssl and not tls.

installed pam_ldap and nss_ldap, they both wanted a proxy user for authentication, and also the admin user for changing passwords.

Tailor http://nautilus.homeip.net/~lele/projects/tailor/ allows syncing between multiple source code control systems, and since there's several projects in unpleasant sccs's i thought I'd try converting them to darcs

• orange

orange certainly looks promising other than the fact they have bugs, don't have doc strings, and lack unit tests. though their tutorials were pretty straightforward.

Unfortunately they're a bunch of OSS windows developers, so their code is sitting in CVS (blech) so I wanted to convert out of it

My first attempts with earlier versions of tailor didn't work so I upgraded to the latest version, and it had problems as well.

What I ended up doing was checking the HEAD out of cvs first, and then telling tailor to convert it to a darcs repo, I don't know if this'll work when they commit something, but it's worth trying.

I used the following to start creating the config file.

$ tailor --verbose -s cvs -R :pserver:cvs@estelle.fri.uni-lj.si:/CVS --module orange -r INITIAL --subdir orange orange > orange.tailor

the file ended up like this

[DEFAULT] verbose = True

[py] target = darcs:targetpy start-revision = HEAD root-directory = /home/diane/src/orange state-file = orange.state source = cvs:sourcepy subdir = orange.cvs

[darcs:targetpy]

[cvs:sourcepy] module = orange repository = :pserver:cvs@estelle.fri.uni-lj.si:/CVS

[csrc] target = darcs:targetc start-revision = HEAD root-directory = /home/diane/src/orange/orange.cvs state-file = orange.state source = cvs:sourcec subdir = source

[darcs:targetc]

[cvs:sourcec] module = source repository = :pserver:cvs@estelle.fri.uni-lj.si:/CVS

• compclust

both chris and I want to try using darcs with compclust but that'll require 2way syncing.

http://www.darcs.net/pipermail/darcs-users/2005-January/005070.html

debian currently has diskless and lessdisks.

Diskless appears to be an NFS root system where apps run on the client Lessdisks is a terminal based system that runs software on the server.

First off we want a version of grub that has has pxegrub apt-get source grub

I then edited the debian/rules file and added the following --enable-diskless (several net cards)

apt-get install lessdisks

I mostly followed along the lessdisks-doc/install

On the router I added the following to dnsmasq.conf (I really should back that bugger up)

# configure network booting #dhcp-vendorclass=pxe,PXEClient dhcp-boot=net:/tftpboot/pxegrub,dara,192.168.1.13

dhcp-option=17,/var/lib/lessdisks #root-path dhcp-option=42,192.168.1.1 #ntp-server dhcp-option=48,192.168.1.13 #font-server dhcp-option=49,192.168.1.13 #x-display-manager dhcp-option=66,dara.ghic.org # tftp-server-name dhcp-option=pxe,67,pxegrub #bootfile-name dhcp-option=69,192.168.1.13 #smtp-server

sigh the pxe client wasn't smart enough to boot off of a different computer than what we started with. So i tried with dara being the dhcp server, i got further but then ran into problems with not being able to load pxegrub from things other than /tftpboot

pxegrub had problems, when i switched to pxelinux.0, installed the default file into pxelinux.cfg (and then copied all of /var/lib/lessdisks/boot into /tftpboot I was able to boot. Unfortunately the kernel they installed doesn't support the ethernet card on my amd64 box.

What do i have to do to get a tftp server to server files off of something other than /tftpboot (or is just the pxeclient that has trouble with it?)

Whee

Spent some time browsing through the linux howtos http://fiona/cgi-bin/dwww?type=file&location=/usr/share/doc/HOWTO/en-html/LDAP-HOWTO/sasl.html

it looks like sasl ships with a number of different auth types with the kerberos stuff split out into sperate modules. The above link documents some information about getting MD5-Digest working with ldap, which should be useful for setting up an ldap auth server.

I forgot to update my xlibs package when upgrading to Xorg so its missing the keymaps necessary to change keyboard settings :( (no caps lock to control mapping)

Another question is should my home net have the wireless VPNed? and if so which protocol? IPSec or OpenVPN

http://openwrt.org/HotspotOpenvpnHowto?highlight=%28Howto%29 Talks about setting up openvpn on the wrt54

One interesting thing that I did do was http://thinkwiki.org/wiki/How_to_make_use_of_Graphics_Chips_Power_Management_features Enable power management of the graphics chips.

Hopefully I the library has free wifi

Home net: what do i want

priority routing for my traffic control / monitering of guest access securing wireless traffic

So I was able to get extensions working in both asterisk and ser.

Asterisk is designed as a PBX so all calls are routed through it, SER is designed like the internet and the router is just a location service. Once a SIP call is initiated through SER it's just the two clients talking to each other.

adding a user in asterisk at the simplest involves adding a sip user for authentication and then binding that user identity to an extension.

In sip the user identity is the extension, however if you want to make it easy for phones to dial the user id you can create aliases using the serctl command.

One major difficulty I had with getting ser working was the registration kept failing. It turns out that its really important for SER to know what all the hostnames its using are so it can know if a request is actualy being sent to itself.

Because my dns server reverse name lookup was broken it wasn't able to determine its FQDN. (there's a reason why you should always list names as "host.domain.name." in the reverse name tables, because if you don't know what you're doing its easy for the default domain to be wrong.

Once I got that fixed SER worked correctly

call transfer worked right too...

The two differnt types of PCAGinsu plots are starting from either 0 or 1.

They should be consistent.

• Meta classses for fun and profit

  www.highenergymagic.org/presentations/metaclasses/

  • are there issues with using __new__ in metaclass?
  • __init__ is much more limited than __new__?
  • do remember to call base class options.

• Quixote 2.0 tutorial

  s = StringForm("foo",

  if request.form:

  value = s.parse(request) retuern "value", value

  else:

  return "<form>%s</form>" % (s.render()

# keywords: exim mail debian

Debian tried changing exim's group and user from mail:adm to Debian-exim:Debian-exim however my old config isn't setting that properly

To get things working temporarily, I changed /etc/logrotate.d/exim4, the group in /var/log/exim4/* and the keys *.crt *.key in /etc/exim4

• Realism of CRN

  • move toward realism

    A+B -K-> X

    X -K'-> A+B (reverse reaction)

  • reversibility

    • equilibrium
    • energy
      • to make things less reversible (lowering k' increases the energy requirements)

  • bimolecular reactions

    • Hard to imagine 5X+12Z+A -k-> A + 7Q as being an elementary step rate constant = k [x]^5 [z]^12 [a] however if the thing forms as a sequence of events the predicted reaction constant would be different.
    • is bimolecular a limited class of reactions that can't accomplish everything we want?
    • the set of bimolecular reactions also includes monomolecular reactions A->B

• reversability A -k-> B

  Energy landscape

    *     Et
      *    *
  Ea    *     *         *
                *     *
           Eb      *
    ----------------------> State Axis
        A         B
    A -(k+)-> B
    B -(k-)->b
  
     k+ = k e ^ (-(Et - Ea)/kt)
     k- = k e ^ (-(Et - Eb)/kt)
  
     since Eb is lower in the energy landscape the k- should be a lower
     rate.
  

  Equillibrium constant Keq = k+/k- = e ^ (-(Eb - Ea)/kt)

  From the diff eqs

  d[A]/dt = 0 = k- [b] - k+ [a]

  at equilibrium [b]/[a] = Keq = k+ / k- ...

  changing the transition energy changes the reaction rate for both the forward and reverse reactions equally. (thus not changing the equillibrium)

• A subclass of CRN:

  • A CRN satisfies detailed balance if: detailed balance :- like equilibrium

    • there exists a function G deg : { X_1, ... X_n } => Real number (Gcirc which operates on a set of chemicals which it assings a real number too) and a scalre RT exists in Real numbers >0
    • for every reaction B with r^B , p^B (reactants and products respectively for each reaction B) there is a reverse reaction B- with r^B- = p^B, and p^B- = r^B ( the products of B are the reactants of B-, and reverse) with k^B / k^B- = e^(-(delta G circ^B) / RT) where delta G cric ^B = Sum(i=1,N) p^B Gcirc(Xi)-r^B Gcirc(Xi) = Sum(i), (p^B-r^B) Gicirc

  • Claim steady states of CRN satisfying detailed balance are called equilibrium states (which implies more than the steady state)

    forall reactions B, k^B Product(i) [Xi]^(ri^B) = k^(B-) Prod(i) [Xi]^(pi^B)

    (restate of the above) and Prod(i) [Xi] ^(pi^B) / Prod(i)[Xi]^(ri^B) = k^B/k^B- = e^(-(delta G circ ^ B)/rt) = Keq

    (Note Gcirc is playing the role of the free energy of the system )

  • detailed balance implies generic steady state but not visa versa 0 = d[Xi]/dt = Sum(B,1,M) k^B (Prod(j)[Xj]^(rj^B)(pi^B-ri^B) - Sum(B,1,M) k^B- (Prod(j)[Xj]^(rj^B)(pi^B-ri^B)

  In this example system there are M forward reactions M reverse reactions B is the reaction

  (Product of the species raised to the power of the number of times the appear)

• Chemistry books can provide information about the standard free energy of a system

                             \Prod(i) [Xi]^(pi^B)
  \delta G \cric ^B = -RT ln -------------------- = -RT ln Kequillibrium
                             \Prod(i) [Xi]^(ri^B)
  

  free energies (not at equilibrium)

                                          \Prod(i) [Xi]^(pi^B)
   \delta G ^B  \delta G \circ ^B + RT ln --------------------
                                          \Prod(i) [Xi]^(ri^B)
  
  
  each species has a free energy
  
  Gi = Gi\circ + RT ln [Xi]
  
  instead of looking at the whole reaction we can look one at a time
  
  note \delta G ^B = \Sum(i) (pi^B-ri^B)Gi
  
  to know if the computation is efficient we need to know the energy
  of the whole system
  
  Gi is mesasured in Kcal/mol eg
  
    moles of Xi = [Xi] * Volume
  
    energy of system  G = \Sum(i) Gi [Xi] V
                        = Sum Gi \circ [Xi] + RT[Xi] ln[Xi]
  
  if you have a steady state with a flow you're using energy, and
  violates detailed balance
  
  detailed balance systems have flows that are exactly the same going
  backwards and forwards. In a detailed balance system All the flows
  eventually go to some point
  

  Criterion

  G always decreases, unless we're at equilibrium

  dG/dt <= 0

  F^B = k^B Product(i) [Xi]^(ri^B) (forward rate) B^B k^(B-) Prod(i) [Xi]^(pi^B) (reverse rate

  P+ = Prod(i) [Xi]^(ri^B) (product synthesized) P- = Prod(i) [Xi]^(pi^B) (product destroyed)

1 dG          d (( Gi\circ  +RT ln[Xi] ) [Xi] )
- -- = Sum(i) --
V dt          dt

     = Sum(i) Gi^\circ d[Xi] + RT \Sum(i) d[Xi] ln[Xi] +[Xi] 1   d[Xi]
                       dt                 dt                [Xi] dt

     = Sum(i) d[Xi] (Gi\circ + RT ln e[Xi])
              dt

     = Sum(i) (Sum(B) (F^B-B^B)(Pi^B-Ri^B)) (Gi\circ +RT ln e[Xi])

     = Sum(B) (F^B - B^B) Sum(i)(Pi^B-Ri^B)(Gi\circ +RT ln e [Xi])

     = Sum(B) (F^B - B^B)(\delta G\circ^B + RT Sum(i) (Pi^B-Ri^B) ln e [Xi])

     = Sum(B)(F^B-B^B)(\delta G\circ^B + RT ln \Prod(i)[Xi]^(Pi^B) + RT Sum(i)(Pi-Ri)
                                                       -----------
                                                       [Xi]^(Ri^B)
                                                                     |- be nice
                                                                        if this
                                                                        was zero -|
     =

   RT ln [Xi] looks like entropy

• Digital Abstraction recap

input exists R => output exists R and

correct possible thanks to restoration: repeater

example : OR

using an or gate with a few inverters that could sharpen the circuit

CRN
      (takes 2 Z1)    Z2
          ---->      |  ^
     Z1   ---->      v  |  (repeat needing 2 copies to catalyze the next reaction)
        ^             Z2*
X-> |   |<-Y
    v
     Z1*

X and Y catalytically change the state of Z1

shows 3d plots of x,y,zi

the first plot shows a position theta where the second reaction is triggered each following reaction pushes the output threshold that's a zero back a little bit further into the region where it is our digital zero.

it works but does require a number of reactions decreasing our efficency

• A hysteretic repeater

  • goal replace simple circuit with another circuit with a much stronger nonlinearity
  • the key realization is that the output is not a function of the input
  • for the digital abstraction as long as the input is valid the output is a function of it, however for invalid inputs there's no
  • hysteresis :- remember the history of the system reason that the output be a function of the input
  • output is function of input for valid input exists Ron or exists Roff otherwise remember the last value. ( while we're in the invalid region) * Is such a thing possible? * helpful to think in terms of vector flow

    Y -
  Ron |                ***
      -
  
      -
  Roff|***
      -
      |---|           |---|
      Roff             Ron
                   X
  

  if we're kicked outside the valid range we'd like the vector to push back to the valid region

    Y -         v
  Ron |      v    *******
      -         *       ^
        .     *  ^      .
        v      ^
           v  v  *
      -        *  ^
  Roff|***  *   ^
      - ^   ^
        .
      |---|           |---|
      Roff             Ron
                 X
  

  the * is the nullclien where d[Y]/dt = 0

  the output gets pushed back to either the top or bottom nullcline depending on which it was historically closer to.

  the nullcline 0 = d[Y]/dt([x],[y])

  the solution is a polynomial which doesn't have breaks so it'll look more like the following.

    Y -
  Ron |                ***
      -           *
              *
            *
              *
                 *
      -     * *
  Roff|***
      -
      |---|           |---|
      Roff             Ron
                   X
  

  Our solution however wont perfectly satisfy the remember the last value constraint, however it'll do it for reasonable peterbations of noise.

  lets find a polynomial and find a circuit

  the 0.5 terms come from shifting the origin to the middle of the s curve.

  ([x] -0.5) = - alpha ( [Y] - 0.5) + gamma( [y] - 0.5)^3

  to translate to a chemical system we just need to collect terms

  (hopefully he chose correctly if the term is wrong it would flip the orientation of all the restoring forces.

   d[Y]                          3  3         2  3                           \alpha   1
   ---- = [X] +\alpha  -\gamma[Y] + -\gamma[Y] -(-\gamma-\alpha)[y]+\gamma/8- ----- - -
   dt                               2            4                              2     2
          |-----------------any value --------------------------------------| |-->0 ---|
  
  ::
  
        \     | \gamma/8 - \alpha/2-1/2
         \    |
          \   |
         ^ \  |
        .   v v  (3/4 \gamma - alpha)
       X     Y  ------------------------>
           .  ^  . .  (using 2 y)
          .   | \ .  \gamma
           .> |  \v
     3/2\gamma    v     \gamma
                  Y+Y+Y ------> Y+Y
       (Y causes its own
       degradation)
  
  . . . represents catalysis
  
  lots of creation and degredation of Y going on here which does well at creating
  our S curve
  
  good design would involve solving the critical points (where the S curve switches
  direction)  (want widly spaced critical points)
  
  
  \partial_deriviate  [X]
  -----------------------   = 0
  \partial_derivative [Y]
  
  (this also forces the existance of critical points, which for some values of \alpha
  \gamma reduces to the simple sigmoid function)
  
  for this example assume
  \gamma/2 - \alpha/2 -1/2 =0
  3\gamma/4 - \alpha > 0
  \gamma > 0
  \alpha > 0
  
  ::
  
       \     | \gamma/8 - \alpha/2-1/2 = 0
        \    |
         \   |
        ^ \  |
       .   v v  (3/4 \gamma - alpha) = 5
      X     Y  ------------------------>
          .  ^  . .  (using 2 y)
         .   | \ .  \gamma
          .> |  \v
    3/2\gamma    v     \gamma = 8
      = 12      Y+Y+Y ------> Y+Y
  

HW

part a:

find the "best" alpha and gamma what's best? you might want the most noise supression the best alpha and gamma are output range os [0,epsilon ] and the input range is [0,delta], find the max delta - epsilon such that the digital abstraction is satisfied

you'll need to find the critical points to determine the max range for Roff and Ron to determine the range delta

part b:

can this design be used to make AND and OR gates w/o extra repeaters is it possible to use the above circuit to construct gates? or can you just take the first CRN in the this day with this circuit as a following repeater?

• So far everything has been feedforward circuits some set of inputs -> gate -> output (no loops)

• feedback circuits can solve systems in much smaller set of reactions

  • allows reuse of circuitry

  • needless to say they're more complicated to build and analyze

  • subclass

    • iterated digital logic

    _      _         _            _
    x -> f(x) -> f(f(x)) -> f(f(f(x)))  -> ...
    

    it might go to zero with all following outputs = 0, (example fixed point)

    • example n-bit counting

      Xn-1 ... X2 X1 X0 are bits of a binary number X we're going to use chemical species Xn-1 ... X2 X1 X0 to represent those bits

    X0  -NOT---->      f0 = NOT X0
        \
    X1 - XOR ---->     f1 = X2 XOR X1
    
    X2                 f2 = (X0 and X1) XOR X2
    
                       f3 = (X0 and X1 and X2) XOR X3
    Xn-1               fn
    
    
    where f(x) = x+1
    
    x    = 110 0111
    f(x) = 110 1000
    

    translate intoi a feedforward CRN that staisfies digital abstraction Given feedforward CRN for f satisfying digital abstraction add clock and latches to compute iterated logic.

    we already have oscillators, what we want now is clock and not-clock

    [clock]        ----     ----
    
    
              ----     ----      -----
                                        t
    
    [clock]    ----     ----      -----
    
    
                   ----     ----
                                    t
    

  (sharp transitions into digital values, there is an invalid period but hopefully we move fast enough through the transitions that no one notices.)

  start with any old oscillator and pass through a set of repeaters to force it into the digital abstraction (and a not gate for the not clock)

  the historetic repeater makes a perfect latch

  latch:

  when clock is high , read input when clock is low , remember last input

  latch Low:

            \       / <... !clock
  X.......>  \     / 1/2
     .        \   /
   clock       v v      5
                L     ----->
           . . ^   . .
            .  |  \ .
             . |   \
               |    \ 8
           12  |     \
                      v
  

  H similar but stable when clock is high Delay line chain

    clock      H1 => L1 => H2 => L2 => H3 ...
    |  low     0  X  1  -> 1  X  0  -> 0
    |  high    0  -> 0  X  1  ->  1  X 0
    |  low     ?  X  0  -> 0  X   1 -> 1
    |  high    ?  -> ?  X  0  ->  0  X 1
  t v
  

  H1 -> L1 -> CRN -> Y1 ->H1

  H2 -> L2 -> implementing -> Y2

  Hn -> Ln -> f(x) -> Yn -> Hn

  clock speed approximately equal to d delta t

• Issues

  • clocks seem unnatural
  • can we build circuits without clocks, in EE asynchronous digital logic is possible (requires latches and handshaking to make sure the system doesnt drift to far out of sync)
  • digital <--> analog
    • is there some way of combining digital and analog to build more powerful systems? (analog systems in the periphery and digital in the core)
  • why binary digital logic?
    • you can have restoration to more than 2 stable states
    • other forms of restoration that give the same advantages but without using digital logic
  • energy and mass
    • do they conserve energy, do they require an influx of food?
  • comparison to biological circuits?
    • biology has its own way of solving some of these problems