David B. Jaffe
Director, Computational Research and Development
Genome Sequencing and Analysis Program
Broad Institute of MIT and Harvard
Most current work: see
ALLPATHSLG.
From 1989 to 2000, I was on the faculty of the UNL Department of
Mathematics and Statistics. In 2000, I took leave to work at the Center for
Genome Research, and in 2002 I resigned my position as Professor at UNL.
I can be reached at jaffe at broadinstitute [DOT] org.
I thank the Department for allowing me to maintain this page.
Most of it is completely out of date. In particular, the
machines cpthree and bigbox are dead.
Online and maintained, believed to be useful
coding theory database
also available in
Macedonian
the complete Split source code and detailed results
Split manual (March 21, 2000), in postscript, same as
"Binary linear codes: new results on nonexistence, 1100 pages, perhaps more
than you want to know about this subject
Weird stuff
Sensory mishmash:
me (remove beard),
my dead cat, my vita,
some ethnic restaurants in Lincoln,
opinionated comments about colloquium talks,
guide to the computer projection equipment in Oldfather 204.
Notcurrent Class Schedule and Office Hours (Spring 2000)
Math 208 (Multivariable Calculus)
9:3010:20 MTWF (OldH 204)
(The class project from last year
Math 208 goes to Venus, is still up,
for your amusement, but not quite functional.)

Math 939
(Algorithms in Biological Sequence Analysis)
4:305:20 MThF (OldH 204). Here was the
course announcement.


Old course materials and course announcements
Before the third millenium, my research area was the existence and
classification problem for optimal binary linear codes. For a more detailed
description of some problems I studied, see
this and the documents shown below.
All my results and examples are encoded in a computer language
Split which I have designed.
If you have viewing or printing problems, look
here or write to me.
Funding from the National Science Foundation
for all this work (grants DMS9623205, DMS9801581) is gratefully acknowledged!


(March 2000)
Numerical results on the asymptotic rate of binary codes
, joint work with A. Barg. Also you might wish to look at the earlier version,
which has graphs in color:
Linear programming bounds on codes of length
1000, "transparencies" for DIMACS talk, report on work (which was) in progress,
joint with A. Barg.
(July 1999) I just put up the following two papers.
Also, the codes
database
has been updated (and moved). I can also put this database on a CD and mail
it to you if you would like (at no charge  it costs me next to nothing), but
I am not sure how to port a database which uses cgi scripts.
Optimal binary linear codes of dimension at most seven,
to appear in Discrete Mathematics. This is joint work with Iliya
Bouyukliev.
The smallest length of eightdimensional binary linear codes with
prescribed minimum distance, to appear in IEEE Transactions on
Information Theory. This is joint work with
Iliya Bouyukliev and Vesselin Vavrek.
Optimal binary linear codes of length <= 30, to appear in
Discrete Mathematics. Updated 11/6/98.
A brief tour of split linear programming,
SpringerVerlag Lecture Notes in Computer Science 1255 (1997), 164173.
Looking inside codes,
Proceedings of the Second International Workshop on Optimal Codes and
Related Topics (Sozopol, Bulgaria, June 915, 1998),
Institute of Mathematics and Informatics (Sofia, 1998), pp. 137143.
[Technical note. Use e.g. Cyclic({1,2,3}) now in place of
Cyclic(1,2,3).]
Binary linear codes: new results on nonexistence, 1100 pages,
version 0.6beta (3/21/2000), ongoing work.
This is the main document for Split. See also
installation instructions and
tips for using
Split.
Some of the data from these documents (and their
provisional successors) is accessible
here,
where you will find a form for entering [n,k]; you will get some information
about [n,k] codes, including thousands of generator matrices, mostly for codes
of dimension <= 12. Last updated 7/23/99.
You can experiment with my program here.
New binary linear codes which are dual transforms of good codes
, preprint.
Computing linear codes and unitals, Designs, Codes, and
Cryptography 14 (1998), 3952. This is joint work with Vladimir Tonchev.
A sextic surface cannot have 66 nodes.
Some coding theory links
Ancient links for finding people:
 Math Departments:
USA,
world
 Phonebooks:
check all US phonebooks (amazing!),
Who's Online (math),
combinatorics,
AMS,
whowhere
 Some people:
Laurinda Jaffe,
Ken Stanley,
Mark Terasaki
Ancient links for making travel plans:
 Time (good luck):
from Australia
 U.S. State Department travel
search engine
 Everything I know about buying
inexpensive airline tickets.
 Boston bed and breakfast: phone 18008880178 or 16175761492.
(Giving e.g. "5761492" to a search engine is a good way to get
related info.)
 Airline information:
United Airlines,
Northwest Airlines (flight info)

Atlapedia country database
 You can get to European rail timetables from
here.
The Netherlands one (NLD) contains a link to an allEuropean rail
computer. (The last time I tried to find this I had trouble, but got
ultimately to it.).
Here is an index
of European railway resources.
 currency conversion
Ancient links for libraries and online databases:
 UNL Library, ...
card catalog, ...
keyword search, ...
title search, ...
author search, ...
journal search, ...
Interlibrary Loan (
journal article,
book).

UNL libraries and beyond: a quick tour from the mathematician's
point of view

MathSciNet  Texas mirror (faster for me) or
MathSciNet  main site; for both you must have a subscription.
 JSTOR (online access to various
mathematical journals)

National Library of Medicine search engine

Bibliography of Fossil Vertebrates
 Library of congress:
homepage,
catalog



