Math and Programming

Fonts and Colors

2011-11-05T20:06:00.000-04:00

Math job search

2011-11-01T20:44:00.002-04:00

Phil Grizzard's detailed description of his job application process.

A Longtime Math Grad Student's Job Search Experience

Totally worth reading if you're on the job market soon. Thanks for sharing!

Gender discrimination?

2011-11-01T20:34:00.001-04:00

Cancer researcher wins gender discrimination suit

From Nature news blog, a few month old.

Git: checkout remote branch

2011-11-01T20:21:00.001-04:00

git checkout -b experimental origin/experimental

Want to review grant applications?

2011-10-17T13:57:00.003-04:00

How to Be a Member of an R01 NIH Study Section

GitX and Finder in MacOs

2011-08-26T09:22:00.004-04:00

GitX is a cool tool to visualize your git branches. It automatically assumes all files ending in .git files are git applications. When you browse files in Finder, anything ending in .git is now not a folder anymore, and clicking on it will launch GitX. Very annoying. I assumed I could just right click the file and set Open with to finder, but you can only change it to other applications, you can't tell your Mac that foo.git is a folder, not a git application. Instead, I edited the file /Applications/GitX.app/Contents/Info.plist (sudo!). Remove the following line inside CFBundleTypeExtensions

<string>git</string>

...
<key>CFBundleTypeExtensions</key>
      <array>
      ~~<string>git</string>~~
        <string></string>
      </array>

...

And then run
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/Support/lsregister -u -r -f /Applications/GitX.app/

It should say
ThrottleProcessIO: throttling disk i/o

Reopening Finder, and foo.git is a nice folder again.

Thunderbird notification pop-up

2011-08-10T13:32:00.000-04:00

Every time I get an email, Thunderbird shows a little pop-up on my screen, saying x new emails from xxx. Oftentimes, I have co-workers look at my screen, they don't need to know everytime I get an email that it's from Amazon, Zappos, Banana Republic, or Victoria's Secret. So, here's how you turn it off:

Click Edit and select Preferences
Click Advanced
Select the General tab
Click the Config Editor button
Search for biff
Set mail.biff.show_alert to false

Mastering Your Ph.D. - Series Index

2011-07-09T09:02:00.003-04:00

Mastering your Ph.D. - Series Index on Sciencemag.org.

Book recommendation: A PhD Is Not Enough: A Guide To Survival In Science

2011-07-09T08:33:00.001-04:00

I've recently read this small book, I devoured the 128 pages within two hours. Thought written in 1993, I think it is still highly accurate.

Feibelman, a physicist, describes several cases of unsuccessful scientific careers, despite hard work and intelligence. He points out the problems and gives advise how to avoid them.

Every scientist should read his book early in grad school, refresh his memory when finishing grad school, and again when mentoring graduate students.

A PhD is Not Enough on Amazon

Academic Job Search: Writing a good CV, research statement, and teaching statement

2011-07-08T19:57:00.005-04:00

I won't give you boring details of how you should format your CV, there's enough resources out there that give you much better advise than I ever could, instead I will tell you what you can and should do during graduate school, to generate the content for your CV and statements.

Please keep in mind that I was specifically looking for post doctoral research positions in mathematical biology. If you want to land a teaching or tenure position, some rules might be different.

Job Application Timeline

Academic Jobs beginning fall 2011 (June – September)
Deadlines for postdocs: as early as November 2010
Asked for letters: September 2010
CV, Research Statement, Preprint/publications/thesis
Draft of Research Statement August/September 2010
CV: first version in 2008, career services, periodically updated
Jobs are advertised on https://www.mathjobs.org/
http://notable.math.ucdavis.edu/wiki/Mathematics_Jobs_Wiki
Discussed everything with my advisor, proof-read by advisor, several friends proof-read my statements, department head, career services
Compared CV and statements to those of other mathematicians

Application Process

Through http://mathjobs.org

Cover letter

Name of position and school
find department head’s name
Possible collaborations/groups, i.e. Mathematical Biology, Symbolic Computation

Mention possible collaboration in research statement

Mention possible new curriculum/teaching methods/undergraduate research in teaching statement

1-3 hours per application

~30 applications

5-10 applications to specific research positions not in Academia:

Research Hospitals, pharmaceutical companies, Microsoft Research, Cancer Systems Biology Group
Application directly to senior researcher

Create Content for your Research Statement

Talk to your advisor (and other faculty) about your goals
Participate in conferences and workshops

Explore local options

SIAM seminar

Department Math Seminars, Physics seminar, Graduate student speaker series, Symposium, … (read all announcement emails!)

Workshops (NSF math institutes)
Poster presentations

Leadership role (SIAM, SGTA, student organization, organize a seminar…)
Letters of recommendation

2-3 research letters, 1 teaching letter
Knows you and your work in detail
Well known
Your advisor can suggest letter writers!

Create Content for your Teaching Statement

“Show, don’t tell”

~~I’m the best teacher in the world.~~
My section scored highest, best rating on evaluations, …

What have you accomplished that distinguishes you from other teachers?

Teaching large/higher-level course?
Anything that’s not standard curriculum (Mathematica)?
Review sessions/material for all sections?
Tutoring? Volunteering with high school events/girls’ math day/Kids’ Tech University?
Do something special now, so you can write about it, when you apply

Tell GTA supervisor about your career goal, he/she might have “special tasks” for you

Special course to teach
Special leadership roles as senior TA

Be a good colleague

Be on time, be prepared
Participate in department events (Visitors’ day, peer mentoring, …)
Be friendly and helpful to your fellow colleagues (share notes, offer to substitute, …)
(especially in a small department) you are hired as a team member, not a 9-5 teacher

My Advice

Have a goal, know what’s necessary to accomplish it, work towards that goal
Take any help you can get, don’t be afraid to ask
Good Luck!

I hope this article makes you start thinking about your CV before you actually have to write one!

Latex: Table of Content problems with Bibliography and Index

2011-07-08T11:31:00.000-04:00

When creating a table of content (TOC) , bibliography and index are not listed when created with \bibliography and \printindex. This is how you get them to appear in the TOC with the correct page numbers.

\cleardoublepage
\addcontentsline{toc}{chapter}{Bibliography}
\bibliographystyle{plain}
\bibliography{../all}

\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{Index}
\printindex

Latex: Centering table larger than textwidth

2011-07-08T11:06:00.000-04:00

Usually, you can center tables with \center. But when the table is longer than the \textwidth, it will be align with the left side margin. You can temporarily adjust the textwidth.

% allows for temporary adjustment of side margins
\usepackage{chngpage}

\begin{table}
    \begin{adjustwidth}{-.5in}{-.5in}
        \begin{center}
        \begin{tabular}{|c|}
            \hline
And here comes a very long line. And here comes a very long line. And here comes a very long line. \\
            \hline
        \end{tabular}

        \caption{This Table is longer than the text width. And its caption is really long, too. This Table is longer than the text width. And its caption is really long, too. This Table is longer than the text width. And its caption is really long, too. This Table is longer than the text width. }
        \label{myTable}
        \end{center}
    \end{adjustwidth}
\end{table}

Changing user's shell

2011-06-10T21:59:00.001-04:00

sudo vi /etc/passwd

Highlighting paragraphs in Latex

2011-06-08T11:00:00.001-04:00

When revising a document, I often want to highlight my changes, so my collaborators can easily see what I changed.

\underline

works for single words, but it puts everything in a horizontal box and long text isn't wrapped anymore.

Instead, I use the package soul and \ul to underline.

\usepackage{soul}

Or you can highlight text using \hl. This will underline the text unless you use the color package, then it turns into typical marker-highlight.

\usepackage{color}

More Proposal wiriting - more favorite words

2011-06-03T12:46:00.000-04:00

coherent conceptual framework
systematize information

OS X: How to Change Default Application to Open File Type

2011-05-09T09:19:00.000-04:00

Wonderful post explaining how to set the default type for a file. Thank you David Kirk!

svn get an old file

2011-03-01T16:17:00.001-05:00

To get the version form the release number 214 :
svn update -r 214 file.sh

Society for Mathematical Biology

2011-02-04T09:52:00.002-05:00

Society for Mathematical Biology

Proposal wiriting - more favorite words

2011-01-17T11:09:00.001-05:00

seek to pioneer new approaches

Preliminary studies hint

novel algorithms

predictive models

software tools for integrative analysis and visualization of genetic interaction networks to facilitate discovery

developing new computational biology

graduate level

highly collaborative, interdisciplinary projects

Analysis & Interpretation

Using a systems biology approach

The methods will be tested and validated in a number of real biological problems

enticing them to pursue careers in science

web-based tools

in silico knockouts

drug intervention can be seen as control of cellular network activity

verification methods to check whether a model is consistent with the laboratory experimental observations on which it is based

If the model does not conform to the data, we suggest a revised model and the new hypotheses are tested in-silico.

The hypotheses formulated during in-silico testing suggest new avenues to explore experimentally.

emerging field of Systems Biology

iterative improvement

sed for several different substitutions in one file

2010-12-27T20:39:00.004-05:00

sed -e 's/a/A/' -e 's/b/B/' <old >new

git merge --squash

2010-12-26T21:37:00.001-05:00

Start out on branch master, then work on an experimental branch

$ git checkout -b experimental

Do a series of commits etc. If you decide that the experimental features should now be part of master, do the following:

$git checkout master
$git merge --squash experimental
$git commit -a

The commit message automatically has a list of all commits in experimental.

Syntax Highlighting on Blogger

2010-12-26T18:06:00.000-05:00

If you change your template, don't forget to include the script tags for syntax highlighting! Follow these simple instructions from

Carter Cole

Uploading a file with JQuery

2010-12-26T17:38:00.013-05:00

You can easily submit data in an html form via jQuery's $.post. But you need to do a little more to upload a file. I suggest the jQuery Form Plugin.

Here is the HTML form:

<html>

<head>

<title>Carter Tomorrow Fund Donations</title>





 

</head>

<body>





</body>

</html>

This is the Javascript file myFrom.js:

And here the cgi script "test.cgi" in Ruby

Make sure that your cgi script has the right permission, 755. Of course you would first manipulate the data instead of just mirroring it.

Happy Holidays!

2010-12-24T11:16:00.006-05:00

Math-Bio-Programming Grant Opportunities

2010-12-22T13:05:00.000-05:00

These NSF/NIH pages have a lot of information on them. Here are a few grant opportunities that might be interesting:

NSF: Advances in Biological Informatics (ABI)

NIH: Innovations in Biomedical Computational Science and Technology

How to get more women in programming

2010-12-12T17:51:00.001-05:00

Not exactly scientific, but some interesting points: Sara Brumfield.

Some famous women in programming

Should I read this? Unlocking the Clubhouse - Women in Computing

Ruby Version Manager

2010-12-08T11:47:00.002-05:00

http://www.rubyinside.com/rvm-ruby-version-manager-2347.html

Since I keep forgetting, it's rvm!

What I just learned not to do:

2010-11-29T18:28:00.000-05:00

to boldly split infinitives that no man had split before.

Pretty flowers in the state space.

2010-11-28T12:05:00.000-05:00

Here is a simple explanation of transients, attractors, and basins: State-space and basins of attraction

Don't they just look like pretty flowers?

My favorite words ...

2010-11-26T20:36:00.001-05:00

... here's my list of words that I'm always struggling to come up with when writing a technical paper:

natural
emphasis
arising in
vital, crucial
innovative
foster
driving
instantaneous
challenge
all aspects of

git status

2010-09-23T14:44:00.002-04:00

git status --untracked-files=no

or

git config alias.stat "status --untracked-files=no"

and then

git stat

I'm trying to trace a bug in some big subversion repository, and decided to put the relevant files under git control. Let's see how that works.

Agent Based Models FTW

2010-09-21T19:20:00.000-04:00

NIH Study Models H1N1 Flu Spread

AT&T disabling unauthorized iPhones

2010-08-23T09:54:00.000-04:00

Dear iPhone,
I love you, but Apple Applies For a Patent To Control Unauthorized Use of iPhones, really?

TDD

2010-08-22T21:58:00.000-04:00

This is a really good book on test driven development. Probably not for somebody who has never tested, but if you have a little testing experience, you'll find it very useful!

`require': no such file to load

2010-08-18T21:17:00.002-04:00

I keep forgetting this:
require 'rubygems'

Rails is painful :(

2010-08-09T01:15:00.001-04:00

LaTeX in HTML

2010-07-28T23:27:00.000-04:00

MathJax

"MathJaxTM is an open source, Ajax-based math display solution designed with a goal of consolidating advances in many web technologies in a single definitive math-on-the-web platform supporting all major browsers."

change ulimit permanently

2010-07-22T11:57:00.000-04:00

When a user changes the limit of system-wide resources with
ulimit -St 36000
this is only valid, for as long, as he is logged in. To set a value permanently, he can edit his .bashrc

ulimit -St 36000

temporary files for testing

2010-07-22T10:02:00.000-04:00

How much cpu time in ulimits?

2010-07-20T15:00:00.000-04:00

You can set the cpu time using ulimit, but to what?
On our 4 quad-core machine, we have set the soft limit to 80 minutes (4800 seconds) but allow the user to increase it to up to two days. On our company wide file server it is set to 20 minutes (1200 seconds).

ulimit - high memory utilization

2010-07-20T14:57:00.001-04:00

If you have too many high memory processes running, your machine probably won't like it. You can set the maximum CPU time per user in

This gives every user 80 minutes of cpu time. You can check with:

If a user needs more cpu (and is aware of that), he can increase it to up to two days but not more than that.

Be careful, ulimit specifies cpu time in seconds, limits.conf in minutes.

Latex: .sty files

2010-07-20T13:15:00.001-04:00

TeX will locate any file in ~/Library/texmf/tex or in a subfolder of this folder; LaTeX will locate any file in ~/Library/texmf/tex/latex or a subfolder of this folder.

For TeXshop on a Mac, .sty files are found in

and all its subfolders.
After placing a new file there, run

to update the entries.

git checkout -b drunk

2010-07-07T19:20:00.001-04:00

This should be safe.

no /proc/cpuinfo on my MAC OS

2010-07-05T15:29:00.001-04:00

Oh no :(

system_profiler SPHardwareDataType|grep "Processor Speed"

Git branches

2010-07-01T12:57:00.001-04:00

Goal for the next 7 days: Use more branches.

M2: keeping track of your ring

2010-06-30T10:26:00.000-04:00

When using a quotient ring, make it a global variable, otherwise you'll end up in the base ring. When you work with a list of polynomials, best store them as a 1xn matrix, this way, they're all in the same ring:

git submodule

2010-06-30T10:20:00.002-04:00

yea, submodules rock!

Rings in M2 with "my variables"

2010-06-25T18:18:00.000-04:00

M2 can easily create a ring with many variables

R = ZZ[vars(0..10)]

But I need my variables to be called x1, ..., x10 (in particular, not x_i)

l = apply(10, i-> value concatenate("x",toString i))

I make strings "xi" and applying value turns the strings into symbols, the correct input for a ring:

R = ZZ[l]
gens R

What I learned today

2010-06-25T18:15:00.000-04:00

Blueskying

No technical terms on user stories, but write the stories out with your "costumer" on cute flash cards.

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

2010-05-20T17:49:00.001-04:00

Science Magazin

Slatest Latest

Die Zeit

Colbert: What makes you think you can do a better job than God?
Venter: We had computers.

Craig Venter on the Colbert Report
2-27-2007

10-30-2007

\@listctr undefined control sequence

2010-05-16T11:45:00.001-04:00

When including special citation packages, but using

latex will complain and not compile the document

Just make sure you comment out the special package

trash the aux files, and you're good to go!

Branching with git

2010-05-11T18:25:00.000-04:00

git branch new-branch
git checkout new-branch

remote push/pull

git-svn

2010-05-08T23:33:00.000-04:00

You can make sure these changes were committed to the svn repository, by doing a svn up in a regular svn clone of the repo. To fetch changes from the svn repo, instead of svn up, do

Installing Lapack on Suse

2010-05-05T18:05:00.001-04:00

Unpack the tar file lapack.tgz.
Copy the Makefile and make it

How to Make a Black & White PDF File

2010-05-05T14:59:00.000-04:00

Open the image with Adobe Acrobat 9 Pro. In the Advanced Tab click on Print Production -> Preflight. Open the menu for PDF fixups by clicking on the triangle next to it and choose Convert to grayscale.

Youtube 500 error

2010-05-04T23:33:00.003-04:00

"500 Internal Server Error Sorry, something went wrong. A team of highly trained monkeys has been dispatched to deal with this situation."

I knew it! Monkeys can program.

Perl 5.8 vs 5.10

2010-05-03T21:35:00.001-04:00

Apparently this used to work in Perl5.8.9 but no in Perl5.10.0 anymore:

$line is empty when run with 5.10.0, but the correct data, when run with 5.8.9. In 5.10.0, omit the extra ${}:

So be careful, when updating to Snowleopard (comes with Perl5.10.0) and your scripts don't work as expected.

crontab

2010-04-26T23:39:00.003-04:00

What you need to know:

Either use the
minute hour day month day-of-week format, or shortcuts like @daily. The script should be placed in /etc/cron with permission to be executable, i.e. 755.

Simple website redirect with perl

2010-04-26T23:09:00.002-04:00

For when you're too lazy to fiddle with mod_rewrite, you can use a simple Perl script to redirect file a.pl to b.pl.

Upload a file a.pl with the following content:

chmod a.pl with the right permissions - and, of course, make sure, Perl is supported.

Nothing better than drunk programming...

2010-04-26T23:05:00.001-04:00

well maybe one thing ...

Setting up remote git repository

2010-04-26T17:59:00.004-04:00

On your remote machine, create a new directory and start a new git repository.

On your local machine, or wherever you have the files, start a git repository, add the files you need, and commit them.

Now you have your files under revision control, but only locally, which is bad if your hard drive breaks or if you work from more than one machine. So add the repository on the remote machine as another remote directory and push to it.

To get the files on another machine, do

converting files to .ps

2010-04-26T11:42:00.000-04:00

You can use Preview -> print -> Save as PostScript to turn a pdf or jpg into ps. Only problem is, that the new image is the size of the paper you printed to, not the original image size. As on the picuture below, there's extra space added at top and bottom of the picture.

Generating ps files from pictures

2010-04-25T14:14:00.001-04:00

If you have, you can use Adobe Acrobat Pro on an image in pdf format and use "Save As" PostScript. If you don't have it, cross your fingers and hope that

works.

No gain from brain training

2010-04-21T10:41:00.000-04:00

I wish, we could always have 11,430 participants for a study as in this Nature article, "No gain from brain training".

The edges of understanding, Arthur D Lander

2010-04-14T17:25:00.001-04:00

"A culture’s icons are a window onto its soul. Few would
disagree that, in the culture of molecular biology that
dominated much of the life sciences for the last third
of the 20th century, the dominant icon was the double
helix. In the present, post-modern, 'systems biology' era,
however, it is, arguably, the hairball."
-- doi:10.1186/1741-7007-8-40

A study of scientific publication ethics

2010-04-09T13:05:00.004-04:00

Just went to a great talk about publication ethics. The next time you review a paper, use this easy tool (eTBLAST) to check for plagiarism. Just copy and paste the abstract to it.

"Identification of duplicate citations in the bio-medical literature
The project aims at identified highly similar citations (based on their abstract) to flag potential cases of unethical publications, using a text comparator algorithm named eTBLAST."

Right now it only searches medical databases (Medline, Pubmed, NASA, ...) but it will search the arXiv soon!

Can a Systems Biologist Fix a Tamagotchi?

2010-04-09T12:59:00.003-04:00

Here's a great paper that humorously lays out the challenges of reverse engineering.

"Another common inspection tool in biology is gene perturbation experiments. As already mentioned, this technique can provide useful information, but it is also used more blindly, e.g., by deleting in turn every single gene in an organism to see what happens. In software engineering, no one has ever seriously proposed to remove each instruction in a program in turn to see what breaks. One might have a slightly better chance of acquiring useful knowledge by removing all pairs or triplets of instructions, but this immediately becomes unfeasible."

Merging multiple files columnwise

2010-04-06T08:47:00.002-04:00

Here's a little parser script, to merge multiple files. Each file has a header and a time course. I need all time courses in a single file, next to each other.

Nature Podcast

2010-04-04T16:44:00.001-04:00

Nature Podcast

Publishing your Thesis

2010-04-04T12:01:00.003-04:00

Dear Igor,

no thank you, my (not yet written) thesis should not be published as a book. The individual sections have been published in different magazines, so it is available to a "wider audience" already. Let's save some trees and not turn every collection of written words into a book.

FH

Dear Hinkel Franz,

I am writing on behalf of the International publishing house, Lambert Academic Publishing.

In the course of a research on the The Department of Mathematics at Virginia Tech, I came across a reference to your work in the field of Mathematics.

We are an International publisher whose aim is to make academic research available to a wider audience.

LAP Publishing would be especially interested in publishing your dissertation in the form of a printed book.

Your reply including an e-mail address to which I can send an e-mail with further information in an attachment

will be greatly appreciated.

I look forward to hear from you.
Kind regards,
Igor Manole
Acquisition Editor

LAP LAMBERT Academic Publishing AG & Co. KG
Saarbrücken
Dudweiler Landstraße 99, 66123 Saarbrücken Germany

Fon +49 681 3720-310
Fax +49 681 3720-3109

i.manole@lappublishing.com / www.lappublishing.com

Handelsregister Amtsgericht Saarbrücken HRA 10752
Partner with unlimited liability:
VDM Verwaltung Aktiengesellschaft

Board of Directors: Dr. Wolfgang Müller (CEO), Christoph Schulligen, Jürgen Gerber, Esther von Krosigk

Supervisory Board: Prof. Dr. Johannes G. Bischoff (Chairman), RA Thomas Bischoff, RA André Gottschalk

Vim Spellchecking

2010-04-04T11:55:00.006-04:00

Vim 7 has built in spellchecking. You can turn it on and off with and F11 and F10 .
To add a word to your dictionary, use zg. But even better, to delete a word from the dictionary, use zw (for wrong word).
You can also manually edit your dictionary, it is in .vim/spellfile.add.

Caption before Label

2010-04-04T11:28:00.003-04:00

If you need to reference a table in a latex document, make sure you set the caption before the label, otherwise the table will be incorrectly referenced as the section it is in.

Latex Table with multirow

2010-04-02T14:32:00.019-04:00

If you ever have to make a table, where you need multiple lines for one entry, this is one way to do it:

Another Macaulay2 Workshop...

2010-03-30T15:13:00.001-04:00

... is coming up.

Workshop Announcement

Macaulay2 Website

Macaulay2 Group

scrolling inside screen

2010-03-30T15:06:00.004-04:00

I love screen, I use it for everything (remote session, slime.vim). But sometimes I hate it. I can't scroll! Well, no that is not true. I didn't know how to scroll.

First you have to turn on the buffer. Create a .screenrc in your home directory with the following content:

You can access the scrollback buffer by entering "copy mode", which is accomplished by typing

Here is the full explanation.

Screen to return to a remote session

2010-03-30T14:18:00.000-04:00

Oftentimes I need to run long computations on a remote machine. Sometimes it's enough to just pipe the results into a text file

In many cases this is not enough, when something goes wrong, or when you need to work with the results, or when you're inside an important irb session and want to come back later. The thing to use then is screen. It allows you to come back, when the ssh connection has been closed, and find your old terminal just the way you left it.

When coming back to the remote machine, you can check on the results:

Movies in Presentations

2010-03-22T22:00:00.007-04:00

Shifting farther and farther away from blackboard talks, I sometimes need animated gifs or movies in my presentations.

And it works perfectly with Latex Beamerclass.

Here is a good tutorial for animated gifs like the one you see. Just make sure, that convert really converted the file to pngs, if not, use Preview and Save As to turn it into the right format.

Here is a wonderful tutorial on including movies. The movie is saved within the pdf file, so no fiddling around with multiple files when giving the presentation using an installed presentation system or a shared laptop.

Before giving the presentation, go through the slides, and click ok on the warning message about playing the movie, then give a wonderful talk!

I used Screen-O-Matic to create a movie. To get rid of the Watermark, you have to pay a small fee - or you make the movie bigger (i.e. longer from top to bottom) than your slide. When you include it in your tex document with

the bottom will be cut off so nobody sees the watermark.

Ruby Best Practices

2010-03-06T15:31:00.002-05:00

There are more chapters available of Ruby Best Practices available.
Chapter 5 is on Functional Programming Techniques, and chapter 6 on When Things Go Wrong. Enjoy!

No space left on device

2010-03-06T15:17:00.003-05:00

An innocent

told me this:

Now, what went wrong? First of all, is it really full?

I guess you could say so. But why? I can track it down with:

And follow it recursively down. A sorted ls gives me the largest file.

Turns out a some script went nuts and created a 30G .gif file.

2010-02-16T13:52:00.002-05:00

I'm sorry it's German, but it's just too funny:

"Diese Vermarktungsstrategie ist hochgradig sexistisch, wer jetzt meint, er könne sich endlich auch mal an einen Roman wagen und "Fucking Karlsruhe: Bekenntnisse eines deutschen Maschinenbaustudenten" verfassen, wird es schwer haben, einen Verlag zu finden." (spiegel.de)

I wish I'd have more time reading

2010-02-04T11:23:00.006-05:00

Weekend Reading: Ruby Best Practice Chapter 1, Driving Code Through Tests

Yes, I'm a little behind with my reading, but it was definitely worth while.

I was happy to find such a good chapter on testing, because most other books only cover trivial testing, but they don't show how to build useful tests.

What did I learn?
* use single tests for every different case. This results in better readability, and in case an assertion fails, I know exactly in which scenario it failed and all assertions in different tests, will be tried, so I'll know right away if all of them failed or just a particular one
* use tests more as a way to drive your software, not only as regression tests
* there's a when? Yes, switch-case is a case-when in Ruby
* goal for next time Ruby programming: force myself to use a stub/mock
* embedding tests in library files

For my math programming (Macaulay2) I rely heavily on tests: for every little function a handful of tests, and a few functional tests, checking the full algorithm. Functional tests are so immensely helpful for math programming, because it's hard to test by hand, if a set of polynomials is exactly the same as expected.

Screen for long remote tasks

2010-01-17T14:03:00.006-05:00

use

to start a session named mySession on your remote machine. Start the things you want to run, for example a

close the shell by quitting terminal (don't Ctrl C out!)
When you come back, and want to see how far your make went, attach to the old screen with

If you don't remember what you called the session, try

Boolean Gröbner Basis in Macaulay2

2010-01-13T18:14:00.001-05:00

Boolean Groebner basis algorithm

Working here

2010-01-12T14:18:00.008-05:00

Now I know where I want to work, it's just a matter of working hard enough to get there.

FedEx Incorrect Adress

2010-01-06T17:13:00.003-05:00

Ordered something and didn't put our house number in front of the street name. So FedEx Tracking shows a Delivery exception - Incorrect address. I quick call to 1-800-463-3339, and a quick conversation with a representative, and they put the correct address in and said it will be delivered tomorrow.

A+ for this costumer service!

Edit: it would have been better, if he'd correctly understood the address, so I called again, and they should deliver soon.

Macaulay2 Workshop

2010-01-06T13:26:00.005-05:00

is happening soon. I hope to gain some new wisdom that will be worth sharing.

Macaulay2 is a software system for research in algebraic geometry - and it rocks, and we were very productive!

obj.send in ruby 1.9

2010-01-05T23:52:00.007-05:00

It might say here, that send doesn't work for private methods in Ruby 1.9, but that's not true anymore. You can also compare the 1.9 and 1.8.6 documentation - identical for obj.send.

Google Analytics and Rails

2010-01-05T11:21:00.002-05:00

Google Analytics and Rails in 60 seconds. Let the tracking begin!

Git pushing to multiple repositories

2010-01-05T10:22:00.007-05:00

If for some reason you have to push to multiple repositories, add an alias to your .git/config (obviously you don't want this in your ~/.gitconfig):

The exclamation mark runs the alias as a command, without an exclamation mark, it's assumed that you run a git command.

results in a change in your ~/.gitconfig

which you can delete with

or delete all aliases.

Syntax Highlighting on Blogger

2010-01-03T00:09:00.000-05:00

easy syntax highlighting for blogger
Works for me.

Vim for irb

2010-01-02T23:20:00.019-05:00

Ever used irb and wished you had safed your commands or could edit them using Vi? Ever tried something new in irb, and then had to painfully copy and paste it to the .rb file? Slime.vim from Jonathan Palardy will be your new best friend.

Slime.vim lets you send highlighted text to a different terminal. This means you can write a few commands, send them to a terminal running irb, notice you want to change something in your first command, modify that line in Vi and resend it to irb, and so on.

Put slime.vim into ~/.vim/plugins

In one terminal:

1. start a named screen

2. name the window

You'll be prompted for the window's name, "Set window's title to:"
irb_window
3. start irb

In a different terminal, start vi and type irb commands, highlight one or multiple commands (ESC V to highlight the current line, ESC vip to highlight a paragraph), type C-c C-c to execute the highlighted text in the other terminal. The first time you'll be prompted for session and window, enter irb_session and irb_window (or whatever name you gave it).

This works for anything in your terminal, I like it for very long commands (using files in some crazy far away subdirectory), Singular, Macaulay2, mysql, and of course irb.

The pink was just a little too much

2010-01-02T14:24:00.001-05:00

Ruby gem for Optimal Control for Conway's Game of Life

2010-01-02T14:08:00.002-05:00

$ gem install optimal-control

http://rubyforge.org/projects/optimal-control/

My little gem to find an optimal control strategy for Conway's Game of Life is available. Documentation will follow ...

Google Sites for quick and easy websites

2010-01-02T14:02:00.005-05:00

I like my (stolen) design, but Google sites is just so much faster - and you barely know it's Google Sites admg.vbi.vt.edu.

And of course we can change the URL, just waiting on the CNAME changes.

Ruby: testing private methods

2010-01-02T13:51:00.032-05:00

Sometimes you want to test a private method. You can make your method public and ignore the principle of encapsulation, or use this nice trick.

As expected, a private method cannot be accessed.

Wait a second. How does that work? Ruby allows you to define methods for an object, a so called singleton method. After instantiating an object, you can define a method for it. Within the singleton method, self is the instantiated object, so you can access its private methods.

Mystery solved.