Diane's World

#tags test,software

Testing the tag module I'm curous how the tag module works for pyblosxom.

TAC 2006 11 02

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

Environmental Capacity Meeting

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

TAC Meeting 2006 Oct 6

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

TAC Meeting 2006, Sept 9

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

SciPy 2006 Day 2

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

SciPy 2006 Day 1

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 (, 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 '
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.

Dr Kam Dahiquist

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)

Special TAC meeting

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

Dialout via bluetooth

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 (, 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.

Qt Mac

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.

TAC Meeting

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 myogenin locus

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/

TAC Meeting

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

Building GHC6 on Arm

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.

Asterisk Frustration

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= 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

Stocastic Grammers

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/

Digging through UCSC

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 (, line 10); backlink
Inline emphasis start-string without end-string.

Brians Repeats

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.

Python & Boost

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 
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.

Pidentd

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

* Showed up at Tony's place and chatted about Arma

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.

SVN

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 [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

Contact tow company directly

to 877-771-0077

Try to figure out power usage

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

DMV Renewal

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

* BioHub prospective user

asked about biohub

show list of orthologs

links to expression array

links to motifs

link to structure

show data source

map viewer

* Getting samba working

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.

Network

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=

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?

So i was trying to get OpenLDAP to work and I kept getting connection errors when I tried accessing over openssl.

$ 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.

* Repository madness

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

There are many different systems for running lightweight clients...

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?)

* Jury Duty

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

Extensions Work

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...

CompClust

The two differnt types of PCAGinsu plots are starting from either 0 or 1.: They should be consistent.

SoCal Piggies

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 "
%s
" % (s.render()

MultiRun

Remember, that the reason you can\'t run a multi-level multirun is because the intermediate clustering algorithms can't pass the parameters further down.

I was originally thinking that the algorithm should look down its list of algorithms and modify its paramemters. Though perhaps instead the wrapper should have some call that allows one to set the next lower algorithms parameters which would then know if it needed to delegate it further down.

exim

# 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

CS 191a

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

CS 191a

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