BMI Students

Eigenfactor

2007-05-10T14:58:00.000-07:00

Rate journals with eigenfactor:link
Blog post about it: link

The economist style guide

2007-04-18T13:04:00.000-07:00

link

Color tools

2007-04-17T10:41:00.000-07:00

Color brewer: link
Adobe Kuler: link
ColorJack:Speher link

Giant photographs of Boston

2007-01-05T07:56:00.000-08:00

Very cool use of google maps

link

PDF printing in Mac OS X

2007-01-05T07:30:00.000-08:00

This was surprising to me, but very useful.

Occasionally I download a PDF and I am not allowed to save it, or even print preview. That's irritating, especially when we have a subscription to that journal -- what exactly did we pay for?

If you go to print, then Preview does give you the option to save as PS. In my experience, this does not work -- I hate PS anyway.

There is a sketchy alternative that worked for me today. Choose print, then Fax PDF, and then choose preview, then save. All this, plus you get the rush of an illicit act, forbidden by a society that could never understand me.

Network effects

2006-12-24T11:49:00.000-08:00

A demonstration of a phase transition in a network -- cool java applet.

http://steinbock.org/netlogo/random_buttons.html

evil brain fungus

2006-12-04T20:39:00.000-08:00

A David Attenborough clip.
link

Postdoc considerations

2006-12-02T15:09:00.000-08:00

An article by Phil Bourne on how to choose a postdoc.
http://dx.doi.org/10.1371/journal.pcbi.0020121

WTF???

2006-09-19T14:01:00.000-07:00

Apparently a company called the Health Discovery Corporation (HDC) owns patents on applying SVMs to biological data and has sued companies that have violated that patent.

HDC holds a large patent portfolio protecting the use of support vector machines in bioinformatics applications.

Searching the patent database, it looks like the relevant one may be
#7062384, but I don't know if in fact that's the one mentioned in the article.

HDC's scientific advisory board includes Vladimir Vapnik, one of the main inventors of the technology, so maybe they do have a moral (in addition to legal) claim on the technology, but it still just feels wrong.

Nature peer review trial

2006-09-14T16:33:00.000-07:00

Nature has started testing its collaborative peer review system
here

3d cell animation

2006-09-04T09:31:00.001-07:00

this company (XVIVO)
worked with harvard researchers to make this video, which is awesome.

Mixing Python and C

2006-08-25T16:51:00.000-07:00

There are a bunch of ways to mix Python and C, including Pyrex (nice technology, but non-standard, so hard to distribute), Boost (never tried it, looks ok), and SWIG (good, but requires some heavy lifting; for large-scale projects), and PyCXX, which Zach mentioned on this blog before (never tried it).

First, before resorting to C, try the excellent psyco module, which gets you a free speedup and requires no work (and if you like the cut of its jib, google for PyPy). The only catch is that psyco is i386-specific.

My preferred way to use C with Python is by actually writing the boilerplate C myself. This sounds stupid/hairy but once you have the minimal code in place, it becomes quite easy to extend. This is especially true if you are doing what I imagine to be the typical Python/C mix: calling a C function from Python with an array to operate on, and getting an array or a number in return (e.g. replacing a slow matrix-operation loop). Smith-Waterman would be a good example; write it in Python, then replace the Smith-Waterman function with C, and verify it is correct by comparing to the Python output, which I assume is correct, but slow, (for instance, it might use easy-to-human-parse strings). I am also assuming that you are using Numeric/numpy arrays and not Python lists, which is likely/advisable for these kinds of number-crunching tasks.

In that spirit, and to save others time I have wasted, below is a very small example C program, a python program that calls it, and a "setup.py" file to build the C shared object that python imports.
More

First, the C code. This code is very simple. It takes the Python Numeric/numpy array as an argument, and its length (you can also null terminate the array). C requires two files to be imported, Python.h, which should be in your path, and arrayobject.h, a Numeric file that may not be in your path (you can copy it into the directory for testing).

Note how the C array is just the data part of the Numeric array cast as int* ( c_segs_array = (int *)segs_array->data; ). At the end of the function a "PyArrayObject" is built from this C array, and returned using "PyBuildValue". The ease of translation between C arrays and Numeric arrays is key, and simplifies the whole process.

Note that c_segs_array must be cast as "char*" for the "PyArray_FromDimsAndData" function.

The second and third functions are boilerplate, and won't change much. No doubt some of this C file is mysterious, but most of it will not change at all. Any function that takes as input a Numeric array or number and returns an array or number can just be slotted into the mintest function.


#include "Python.h"
#include "Numeric/arrayobject.h"


static PyObject *
mintest(PyObject *self, PyObject *args, PyObject *kwargs) {

  //-----------------------
  //List arguments/keywords
  //-----------------------
  static char *kwlist[] = {"py_segs","num_segs",NULL};

  int i;

  int num_segs;
  int dims[1];

  PyObject *py_segs;
  PyArrayObject *segs_array;
  int *c_segs_array;

  //---------------
  //Parse the input
  //---------------
  if (!PyArg_ParseTupleAndKeywords(args, kwargs, "Oi:nothing", kwlist, 
                                   &py_segs, &num_segs)) {
        return NULL;
  }

  //-------------------------------------------
  //Make C arrays from my python numeric arrays
  //-------------------------------------------

  segs_array = (PyArrayObject *)PyArray_ContiguousFromObject(py_segs, PyArray_INT, 0, num_segs);
  c_segs_array = (int *)segs_array->data;


  for (i = 0; i < num_segs; i++) {
        fprintf(stderr,"C testing %d\n",c_segs_array[i]);
  }

  //----------------
  //Return the array
  //----------------
  dims[0] = num_segs;
  PyArrayObject *return_array = (PyArrayObject *)PyArray_FromDimsAndData(1,dims,PyArray_INT, (char*)c_segs_array);
  return Py_BuildValue("Oi", return_array, num_segs);  
}


static PyMethodDef mintestMethods[] = {
    {"mintest", (PyCFunction)mintest, METH_VARARGS|METH_KEYWORDS, 
     "HELP for minimal_test\n"},
    {NULL,NULL,0,NULL} /* Sentinel -- don't change*/
};

PyMODINIT_FUNC
initmintest(void) {
    (void) Py_InitModule("mintest", mintestMethods);
    import_array();
}

Now setup.py. This is simply a distutils file that tells python how to build the C file. Like with any python module, you type "python setup.py build" to build it, and "python setup.py install" to install. For testing, I usually just build it (which makes a build directory), then make a symbolic link in the main directory (ln -s build/lib.linux/mintest.so mintest.so).


from distutils.core import setup,Extension

module1 = Extension('mintest',sources=['mintest.c'])

setup(name = 'mintest',
        version = '1.0', 
        description = 'minimum C test', 
        ext_modules = [module1])


#extra_compile_args = ["-O4"]  # You could put "-O4" etc. here.

Finally, the Python program, which is hopefully self-explanatory.


import os, sys, re
import random
import Numeric as N
import mintest

#Make a 1D array of length 10
pyarray_length = 10
pyarray = N.array([random.randrange(100) for i in range(pyarray_length)])

#Print out the array as Python sees it
print "Python printing array", type(pyarray), pyarray, pyarray_length

#Get the same array after passing it to C and back
carray, carray_length = mintest.mintest(pyarray, pyarray_length)

#Finally print out the returned array
print "Array after going through C", type(carray), carray, carray_length

And that's it! Pretty easy once you know how.

infosthetics

2006-08-22T15:40:00.000-07:00

Following on from Zach's junk charts post, this infosthetics blog is sweet.
www.infosthetics.com

ANSI Escape Codes in Python

2006-08-05T12:28:00.000-07:00

ANSI escape codes are surprisingly useful. For Python, the escape code is "\x1b[". Here is an example loading bar. This is a Unix thing, won't work on windows.


sys.stderr.write("\x1b[34mloading[" + " "*10 + "]\x1b[0m\r")
sys.stderr.write("\x1b[8C")
for i in range(10):
   sys.stderr.write('.')
sys.stderr.write('\n')

Here "\x1b[34" is "colour foreground red", and "\x1b[8C" means move the cursor right 8 spaces"

It prints out something like this, but with loading in red:
loading[..........]

http://en.wikipedia.org/wiki/ANSI_escape_code

Lectures on Interpreting High-Dimensional Data

2006-06-13T15:42:00.000-07:00

Eugene Fratkin in Seraphim's lab sent me this link: Mathematical and Statistical Methods for Visualization and Analysis of High Dimensional Data. Each lecture has a link to download the video in various formats.

Nature's "open" peer review trial

2006-06-13T00:02:00.000-07:00

Nature is testing the waters of a paradigm-shifting peer review process, where submissions can be displayed for the general public to see and comment on before acceptance. Three cheers for forward thinking where I didn't expect it!

Upon further investigation of PLoS One, I think it's in a similar vein. I've always been excited about this idea but am (pleasantly) surprised that it's actually happening so soon.

PLoS ONE

2006-06-08T20:46:00.000-07:00

I haven't read the whole thing yet, but PLoS ONE looks like it's going to be very interesting....

link

PCA and Friends: A useful review

2006-06-08T20:32:00.000-07:00

Here is a potentially-useful review of PCA and other "geometric methods for feature extraction and dimensional reduction" (that's the paper title). It's by Chris Burges, who has done some nenat machine-learning work at Microsoft Research. The selection of algorithms reviewed is a bit limited by what Burges thinks is cool/useful and what he has used in the past, but hey, that's probably an OK criterion.

[Update: eliminated claim Burges invented SMO when really it was John Platt.]

Pharma...

2006-06-07T19:40:00.000-07:00

A scary article on pharma and clinical trials.

Money quote:
As Dr. Marcia Angell, a former editor of The New England Journal of Medicine, noted in the Baltimore Sun, "What would be considered a grotesque conflict of interest if a politician or judge did it is somehow not in a physician."

link

Humans and chimps

2006-06-03T13:30:00.000-07:00

Jimmy: I have a crazy friend who says humans and chimps are related. Is he crazy?
Troy: No, just ignorant. You see, your crazy friend never heard of "The Bible." Just ask this scientician.
link

Phages

2006-05-30T18:33:00.000-07:00

Slate has an interesting article on the use of bacteriophages to attack infections instead of antibiotics. They also speculate that unfortunately it will be hard to bring the technology to the US.

link

Notes on classifiers

2006-05-20T18:19:00.000-07:00

I have been testing a bunch of classifiers for a project I am doing. The objective is to classify an intergenic region as ACE1 (or any motif) or not-ACE1, based on features of the intergenic regions. I did this for a number of sets of features, and the results were very consistent. I have done enough tests that I feel comfortable relating some general conclusions....

Random Forests and SVMs always won, with random forests usually commanding a slight lead. SVMs with a polynomial kernel did a bit worse. MaxEnt usually came fourth, and seemed to do better on discrete data (hence the NLP slant of this method). Finally, k-nearest neighbors always lost. Random Forests were slower than SVMs, apart from that I think they are preferable.

Random forests are just collections of voting decision trees, each trained on bootstrapped data and variables. Someone must have done the same thing for collections of voting SVMs. If I find it I'll add it to this post. Seems like it must win overall.

Flowers that detect landmines

2006-05-15T17:23:00.000-07:00

This kind of thing helps GM food's image no end...
link

LaTeX

2006-05-13T13:06:00.000-07:00

I use LaTeX a lot, mainly because Word on the mac is so horrible, and I like not worrying about formatting while typing. This article explains some of the small benefits of doing so.

link

Mammalian promoters

2006-05-02T14:11:00.000-07:00

Nature Genetics just published a milestone paper from the Fantom/RIKEN consortium compiling an enormous genome-wide collection of transcript start sites (TSSs) in humans and mice. The paper could be a treasure trove for bioinformaticians. They collected TSS tags from many different tissues and mapped them onto the genome. There are several different classes of promoters: some with very well defined TSSs, some with very broad distributions (transcription can start anywhere in a comparatively broad region), some with mutliple well-defined sites and some with combinations of the above. The paper claims four classes. I don't know what kind of clustering they used -- but it would be interesting to know more about how distinct their classes are and if four is really the best estimate.

I think that in addition to analyses they did in the paper, one can try a bunch of correlations quickly -- several possibilities for projects small and large. Like, do promoter classes correlate with alternatively spliced genes? or are TSS'es correlated with transcription units from tiled array experiments (Affy and others)? One can also do some gene ontology correlations, or expression analysis using these data. We know that transcription initiation, splicing and expression (and other things) are all intimately connected, so this might be leveragable in many different directions...

Machine learning videos

2006-05-01T09:50:00.000-07:00

There are a bunch of machine learning webcast lectures here. Many of them are tutorials; includes a few biology-focused lectures.

link

Good and bad information design blog

2006-04-25T23:32:00.000-07:00

They have some interesting and potentially useful commentary on bad (and good) newspaper (&c.) infographics at Junk Charts.

path.py: Useful python module for manipulating files.

2006-04-20T11:07:00.000-07:00

Check out this path manipulation module. It looks quite handy, as it bundles a bunch of path-related things from the python standard library into a convenient class.
Here's a very simple example.

(Old)

import os
path = '/foo/bar/baz'
files = [f for f in os.listdir(path) if f.endswith('.txt')]
fullpath = os.path.join(path, 'hello.py')
f = open(fullpath, 'r')
lines = f.readlines()

(With path.py)

from path import path
path = path('/foo/bar/baz')
files = path.files('*.txt')
fullpath = path / 'hello.py'
lines = fullpath.lines()

The Science of Scientific Writing

2006-04-13T17:37:00.000-07:00

Some concrete examples on how to write better; concrete!

link

Academic search

2006-04-12T09:28:00.000-07:00

academic.live.com just launched. It's a citeseer/google scholar-like search by MSN.

On the installation of a proper Python environment

2006-04-10T15:39:00.000-07:00

I recently had my hard drive fail, so I have just had the fun of reinstalling my Python environment from scratch. Here are instructions for setting up Python as a proper interactive development and data analysis environment. Some of these instructions are OS X specific (I'll flag those), but the general procedure will work on any *nix-ish platform.

Note that on OS X, I don't really love Fink or Darwinports for building and installing software for me. Especially not software that I depend on, and may need to patch, or use bleeding-edge versions, etc. So, here is how to install the following, all from source:

Python -- The best.

IPython -- An interactive python shell. Really useful.

NumPy and SciPy -- Numerical and scientific computing packages. Key for serious Python data analysis.

Gnuplot -- This is the plotting package that I use, and that I actually really like. (Hint: it saves plots as SVG for editing in Illustrator.)

Gnuplot.py -- A Python to Gnuplot bridge.

Here are the installation instructions.

Before doing anything, make sure that /usr/local/bin is first in the PATH environment variable, because that's where we'll be installing these things. To see your path, type echo $PATH, and you will see a colon-separated list of directory names. This list or directories is searched, in the order specified, for programs to execute when you type in a particular name, like python. Since we are leaving Apple's own old (and crappy) version of Python in /usr/bin, we need to make sure that the new shiny Python we install (in /usr/local/bin) will be the one that is used when we type python into the shell. Hence the need to put /usr/local/bin first on the PATH.
If you need to add /usr/local/bin to the PATH and you're using the bash shell (the OS X default), you will need to create a file called .profile in your home directory (if it doesn't exist) and add the following line to it: export PATH=/usr/local/bin:$PATH. Here's a good way to do that:

echo "export PATH=/usr/local/bin:$PATH" >> .profile

If you're using tcsh (you would know if you are since it's not the default; but you can type echo $SHELL to find out), you would want the following:

echo "setenv PATH /usr/local/bin:$PATH" >> .tcshrc

Also note that I've only tested this on OS X 10.4. Some of the stuff might not work right on 10.3. Finally, If you're using 10.4, make sure that you have the latest version of the developer tools.

And now, the directions!

Make a directory for the source code we'll be getting.
```
cd ~
mkdir Developer
cd Developer
```

Install GNU Readline. This library allows Python and other programs to use the arrow keys like you expect, and many other goodies. Most *nixes come with a good version of Readline, but Apple doesn't ship OS X with one, probably because it's GPL. We'll install the latest Readline, plus some patches to it that are pretty important to make IPython work.

curl -O ftp://ftp.cwru.edu/pub/bash/readline-5.1.tar.gz
tar -xzf readline-5.1.tar.gz
cd readline-5.1
curl -O ftp://ftp.cwru.edu/pub/bash/readline-5.1-patches/readline51-001
curl -O ftp://ftp.cwru.edu/pub/bash/readline-5.1-patches/readline51-002
curl -O ftp://ftp.cwru.edu/pub/bash/readline-5.1-patches/readline51-003
curl -O ftp://ftp.cwru.edu/pub/bash/readline-5.1-patches/readline51-004
cat readline51* | patch
./configure
make
sudo make install
cd ..

Now Python 2.4.3 (the latest released version). These instructions are specific for building Python as an OS X framework (the proper way to install Python on OS X.)
```
mkdir Python
cd Python
curl -O http://www.python.org/ftp/python/2.4.3/Python-2.4.3.tgz
tar -xzf Python-2.4.3.tgz
cd Python-2.4.3
./configure --enable-framework
make
sudo make frameworkinstall
cd ../..
```
If you're using tcsh, you'll need to type "rehash" so that the shell can find the just-installed python.

Now we need to get Subversion (a CVS-like tool) to check out bleeding-edge versions of IPython, SciPy, and NumPy. (Trust me, the svn versions of these are better than the latest releases, and more bug-free, because I've been actively tracking down OS X bugs for these tools.)
These instructions show how to (on OS X) download a .dmg disk image containing a .pkg installer, mount the image, install the package, and unmount the image, all from the command line. You could also just do it from the finder with double-clicking, but this shows how hard-core I am!
```
curl -O http://metissian.com/downloads/macosx/subversion/subversion-client-1.3.1.dmg
hdiutil attach subversion-client-1.3.1.dmg
sudo installer -pkg /Volumes/Subversion\ Client\ 1.3.1/SubversionClient-1.3.1.pkg -target /
hdiutil detach /Volumes/Subversion\ Client\ 1.3.1
```

Now IPython. The "pythonw" part is OS X-specific (see the IPython manual for explanation), on other platforms just use "python".
```
cd Python
svn co http://ipython.scipy.org/svn/ipython/ipython/trunk ipython
cd ipython
sudo pythonw setup.py install --install-scripts=/usr/local/bin
cd ..
```
Don't forget to type "rehash" if you're using tcsh, otherwise the shell won't be able to find the newly-installed ipython script.

Now NumPy.

svn co http://svn.scipy.org/svn/numpy/trunk numpy
cd numpy
python setup.py build
sudo python setup.py install
cd ../..

Here's a fun one. Apple ships GCC version 4 with Tiger. GCC 4 is OK, but it changed the standard for linking object files together from how GCC 3 did it. Now, we'll need to link together a lot of C and Fortran code for SciPy (which wraps lots of high-performance numerical libraries, which are mostly written in Fortran). So we'll need to use a single linking style -- that of gcc3 or of gcc4. Now g77 is the GNU fortran compiler that works with gcc3, and gfortran is the one for use with gcc4. Unfortunately, gfortran sort of sucks, in that it is known to generate incorrect code, especially for PPC chips. So, unless you've got an Intel Mac, we will have to use gcc3 and g77. (The gcc3 Apple supplies for Intel macs is known to suck, so on Intel you should use gcc4 and gfortran.)
Anyhow, this means that we'll need to tell gcc to use version 3 and not version 4 for the code we compile to link with scipy. Skip if on an Intel Mac. Also skip if you're on OS X 10.3, because gcc3 is all you've got in that case.
```
sudo gcc_select 3.3
```

Now we install FFTW (version 2, which is what SciPy needs). FFTW is a library for doing Fourier transforms.

curl -O http://www.fftw.org/fftw-2.1.5.tar.gz
tar -xzf fftw-2.1.5.tar.gz
cd fftw-2.1.5
./configure
make
sudo make install
cd ..

Now we get the Fortran compiler (this is OS X-specific). We'll just grab a pre-built binary of the compiler, since even I agree that compiling a compiler is overkill.
For PPC Macs:

curl -O http://easynews.dl.sourceforge.net/sourceforge/hpc/g77v3.4-bin.tar.gz
sudo tar -C / -xzf g77v3.4-bin.tar.gz

For Intel Macs:

curl -O http://easynews.dl.sourceforge.net/sourceforge/hpc/gfortran-intel-bin.tar.gz
sudo tar -C / -xzf gfortran-intel-bin.tar.gz

Now we compile SciPy.
```
cd Python
svn co http://svn.scipy.org/svn/scipy/trunk scipy
cd scipy
python setup.py build
sudo python setup.py install
cd ../..
```
If for some reason you have both g77 and gfortran installed, and want to choose which one to use, the build line looks like:
```
python setup.py config_fc --fcompiler=XXX build
```
where XXX is gnu (for g77) or gnu95 for gfortran.

Now we can revert back to the default GCC version. (Skip on Intel Macs. Also skip on Macs running 10.3, since they don't have gcc4 anyway.)
```
sudo gcc_select 4.0
```

Now, install AquaTerm. This is a graphics terminal for Gnuplot to use that is very nice for OS X, and way better than using the X11 terminal, I promise. (It's anti-aliased, for example.)

curl -O http://easynews.dl.sourceforge.net/sourceforge/aquaterm/AquaTerm1.0.0.dmg
hdiutil attach AquaTerm1.0.0.dmg
sudo installer -pkg /Volumes/AquaTerm/AquaTerm.pkg -target /
hdiutil detach /Volumes/AquaTerm

Now we grab a CVS version of Gnuplot (the CVS has better OS X support). The Sourceforge CVS servers are sometimes overloaded, so you might need to repeat these commands a few times until they succeed. (Thanks Brian for pointing this out.)

cvs -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/gnuplot login
[press enter to leave a blank password]
cvs -z3 -d:pserver:anonymous@cvs.sourceforge.net:/cvsroot/gnuplot co -P gnuplot
cd gnuplot
./prepare
./configure
make
sudo make install
cd ..

Last step! Install Gnuplot.py. Now, this library is designed for Numeric, which was NumPy's predecessor. So to make things work, we'll use a NumPy tool to fix the Gnuplot.py code, and do some search-and-replace to fix things that the numpy tool doesn't fix currently. (Ugh!) Note that in an earlier version of these instructions, the python command line was python -c 'import numpy.lib.convertcode; numpy.lib.convertcode.convertall()'. This has changed with recent versions of numpy.
```
cd Python
curl -O http://easynews.dl.sourceforge.net/sourceforge/gnuplot-py/gnuplot-py-1.7.tar.gz
tar -xzf gnuplot-py-1.7.tar.gz
cd gnuplot-py-1.7
python -c 'import numpy.oldnumeric.alter_code1; numpy.oldnumeric.alter_code1.convertall()'
sed -i -e "s/Float32/float32/g" *.py
sed -i -e "s/Float64/float64/g" *.py
sed -i -e "s/Float/float_/g" *.py
sudo python setup.py install
cd ../..
```

OK! Now how to use all of this stuff? Well... that's for a later post. Here's a hint, and a test to make sure everything works.
Run ipython, and then try the following:
import numpy, scipy, Gnuplot num_steps = 20 range = numpy.linspace(0, 2 * numpy.pi, num_steps) sin = numpy.sin(range) print range print sin g = Gnuplot.Gnuplot() # Gnuplot expects list of [x, y] pairs, not [x-list, y-list] points = numpy.transpose([range, sin]) g.plot(points) # Feed text straight to Gnuplot to control plotting style. g('set data style linespoints') g.replot() # Fit a spline to the original data and interpolate the curve with finer spacing import scipy.interpolate spline = scipy.interpolate.InterpolatedUnivariateSpline(x = range, y = sin) more_steps = 200 new_range = numpy.linspace(0, 2 * numpy.pi, more_steps) interpolated = spline(new_range) g.plot(numpy.transpose([new_range, interpolated])) true_values = numpy.sin(new_range) error = interpolated - true_values g.plot(numpy.transpose([new_range, error])) print "RMS Error = ", numpy.sqrt((error**2).mean())

Folding DNA to create nanoscale shapes and patterns

2006-04-04T18:32:00.000-07:00

oooh this paper is cool...
link

Mac shortcuts

2006-04-04T18:00:00.000-07:00

A couple of shortcuts I learned recently.

Ctrl-command-D while hovering over a word, will give you a dictionary definition.
Shift-command-4 gets a screenshot of a selection.
Shift-command-3 gets a screenshot of the whole screen.
Alt-command-= zooms in.
Ctrl-alt-command-8 funketizes.

DSA keys

2006-03-27T21:43:00.000-08:00

RSA/DSA keys are great because typing in you password every time is so tedious, especially if you do a lot of scping. I do it rarely enough that I always forget how to set it up and have to scour the interweb for it.

On the computer you are sshing from:
ssh-keygen -t dsa
I don't use a passphrase. I don't think it really matters.
Then
scp .ssh/id_dsa.pub brian@other_computer:./.ssh/authorized_keys

If authorized_keys already exists you'll want to append to that file....

Idea market

2006-03-27T05:56:00.000-08:00

The NYTimes has a good article on a "stock market" for ideas and how companies are starting to do this. I think Google already does this.

http://www.nytimes.com/2006/03/26/business/yourmoney/26mgmt.html?pagewanted=1&ei=5090&en=0d90ed5116e769d0&ex=1301029200&partner=rssuserland&emc=rss

An interesting company they mention in InnoCentive...a company that posts chemistry and biology problems from companies with a reward for the group that solves it.

http://www.innocentive.com/

Javascript tutorial

2006-03-14T18:45:00.000-08:00

This is actually a pretty good reference. I've been writing stuff in Javascript since last summer and have read two books on it, but there is still a bunch of useful stuff in the tutorial i didn't know about. Which is weird because Javascript is a pretty small language.
link

Tom Rando's awesome talk

2006-03-10T11:34:00.000-08:00

Tom Rando gave last Wednesday's Frontiers talk and it was really good. He works on muscle growth and regeneration and the title of the talk was "Aging, stem cells, and the challenge of senescent tissue repair". Aging and stem cells -- double sexy based on the title alone, but the content was even better.

I am not going to summarize the presentation in detail, but will list three of the coolest things I learned during it. First, apparently, one can do parabiotic experiments, which involves connecting two organisms subcutaneously. After a while (days or weeks), the vessels of the two organisms find each other and they start merging their circulatory systems. In Rando's experiments they attached mice from different age groups and studied the effects of young blood on old mice and vice versa. What they found (this is the second cool thing) is that stem cells that are responsible for muscle regeneration after injury are present and are totally fine in the old mice. It's just that the younger mice have some kind of a factor in their blood serum that stimulates the stem cell activation, while the old mice appear to be saddled with inhibitors. Joining a young mouse with an old one restored muscle regeneration in the old mouse completely. They also did some in vitro experiments to further understand what's going on. Pretty neat.

The last thing that kind of blew my mind, was this idea first proposed by Cairns in 1979, that through successive rounds of DNA replication the organism remembers which strands are the original ones and which ones are copies. These template strands are segregated together and find themselves in the same cells. This allows the organism to preserve the original code and withstand the mutational load in tissues with a lot of regeneration (most errors come about as a result of synthesis). It seems like initially no one could find any support for this hypothesis, but now Rando and others have presented some pretty convincing evidence based on DNA labeling experiments. I guess you needed to know where too look -- stem cells are the ones that carry the template DNA and there aren't that many of them relatively speaking.

While I don't know if there is anything informatics-related in what Tom Rando does but he is at Stanford, and is doing some of the coolest work around.

Viruses

2006-02-17T18:40:00.000-08:00

"""If you put every virus particle on Earth together in a row, they would form a line 10 million light-years long. """

That seems like rather a lot of viruses.

discover magazine article

Bio-ontologies

2006-02-17T11:23:00.000-08:00

A blog post about the Nature Biotech article that criticized bio-ontologies, featuring our very own Mark Musen.

Via postgenomic.

nodalpoint

New metablog thing

2006-02-16T13:07:00.000-08:00

I don't know what it is exactly, but I like it.

Postgenomic aggregates posts from life science blogs and then does useful and interesting things with that data.

postgenomic

Uniquifying a list in Python

2006-02-11T19:03:00.000-08:00

I keep needing to do this all the time (given a list, remove all the duplicates). So a one-liner:
dict().fromkeys(yourlist).keys()

Advice for getting published

2006-02-02T18:59:00.000-08:00

10 simple rules from Phil Bourne over at PLOS Comp Bio. They are mostly common sense, but make for some useful reading anyway.

Trends in Machine Learning

2006-02-01T11:41:00.000-08:00

Some graphs showing trends in the use of SVMs/naive Bayes/expert systems etc.
Link

Similar for bioinformatics.
Link

Bagelblog

2006-01-31T20:38:00.000-08:00

Nice post by Serge.
Link

For the pythonistas out there

2006-01-31T14:59:00.000-08:00

A very nice reference for Python 2.4. Good to keep handy.
link

More expertise

2006-01-30T11:56:00.000-08:00

Following up on expertise, it seems like throwing darts at a stock ticker is as good as using mutual funds. I wonder if someone has worked out the expected return from using a random fund compared to random stock choices...
Link

Viruses/Germs vs genes

2006-01-30T11:36:00.000-08:00

A virus makes you fat?
A virus makes you autistic?
A germ makes you gay?
A germ makes you schizophrenic? (Remind me not to go near cats).
Maybe, maybe not, but viruses/germs are ubiquitous and genes are not the be all and end all.

Also I would like to take this opportunity to coin the word "germes" for foreign DNA/parasites that have effects that seem indistinguishable from genetic. For good measure, I also coin "germome", and "germetics", and "germealogy" (yes, that's how you spell it).

Start using these words immediately.

The best place to work...

2006-01-18T15:48:00.000-08:00

is Genentech, apparently.
link

Brains are Bayesian

2006-01-16T15:54:00.000-08:00

Economist article
Nature paper

Clickworkers

2006-01-16T15:52:00.000-08:00

NASA uses humans to find craters on Mars. I wonder how this would work for tumors, or other cell classification tasks....
Clickworkers

13 things that do not make sense

2005-12-31T16:43:00.000-08:00

An article in New Scientist. The first thing that makes no sense is the placebo effect, which may or may not be real.

Bioweka

2005-12-28T15:12:00.000-08:00

An extension to weka for bioinformatics exists. Their added feature list is impressive.

Bioweka

Wheat

2005-12-27T13:48:00.000-08:00

A fascinating history of wheat in the Economist. Link. Also: Golden rice

giftornot.com

2005-12-13T14:28:00.000-08:00

Many real alive people are writing articles about this gift ideas website. I endorse this product.

Forecasting

2005-12-11T14:46:00.000-08:00

An interesting New Yorker article on forecasting and ostensible expertise.

There are also many studies showing that expertise and experience do not make someone a better reader of the evidence. In one, data from a test used to diagnose brain damage were given to a group of clinical psychologists and their secretaries. The psychologists’ diagnoses were no better than the secretaries’.

link

Spicy food and cancer

2005-12-06T10:53:00.000-08:00

This article has some interesting statistics about cancer and spicy/Indian food. At least something that's good for cancer tastes good... Good blog too.

NY Times articles

2005-12-04T12:12:00.000-08:00

I recently found out that you can read an NYT article all on one page, by adding ?pagewanted=all to the end of the url. This bookmarklet also does the trick.

javascript:if%20(location.href.indexOf('?')>0){location.href+="&pagewanted=all"}else{location.href+="?pagewanted=all"};

Using Curl for fast downloads

2005-11-29T17:05:00.000-08:00

This is nice, although I am rarely waiting on downloads these days.
From here.

For example, suppose you want to download the Mandrake 8.0 ISO from the following three locations:
url1=http://ftp.eecs.umich.edu/pub/linux/mandrake/iso/Mandrake80-inst.iso
url2=http://ftp.rpmfind.net/linux/Mandrake/iso/Mandrake80-inst.iso
url3=http://ftp.wayne.edu/linux/mandrake/iso/Mandrake80-inst.iso

The length of the file is 677281792, so initiate three simultaneous downloads using curl's "--range" option:
bash$ curl -r 0-199999999 -o mdk-iso.part1 $url1 &
bash$ curl -r 200000000-399999999 -o mdk-iso.part2 $url2 &
bash$ curl -r 400000000- -o mdk-iso.part3 $url3 &

Machine learning blog

2005-11-14T18:42:00.000-08:00

At this machine learning blog, they scanned in a number of old papers, including:

"Why isn't everyone a Bayesian?" by Efron B, American Statistician 1986. Examines reasons why not everybody was a Bayesian, as of 1986, with scorching reply from Lindley.
"Axioms of Maximum Entropy" by Skilling, MaxEnt 1988 proceedings. Sets up four practically motivated axioms, and uses them to derive maximum entropy as the unique method for picking a single probability distribution from the set of valid probability distributions.

The other posts are worth a look too.
Here

Personal Genome Project

2005-11-14T18:35:00.000-08:00

George Church comments on a Personal Genome Project...
Here

The FDR

2005-11-04T14:37:00.000-08:00

False Discovery Rate is really important for most of us. This paper (lecture notes, actually) covers most of what you need to know. Gil Chu recently gave a talk on local FDR, so I am linking to that paper too. The first link's server seems to be down right now (hopefully temporarily). Anyone know what the difference between local FDR and PER is?

Multiple Hypothesis Correction
Review from Genome Res.
Local FDR

Nature podcast

2005-10-24T22:47:00.000-07:00

The Nature podcast is sweet.

Nature podcast

2005-10-24T15:41:00.000-07:00

Nature now has a podcast, and it's pretty good.
http://www.nature.com/nature/podcast/index.html

Typefaces

2005-10-18T17:37:00.000-07:00

Choosing typefaces can be stressful, and if you are not careful you could end up using Comic Sans, or Arial (this is Zach-style font snobbery, the most enjoyable kind). That's why I have made a list of fonts I can refer to. For those unaware, serif is better for long strings of text, particularly printed text; it's less tiring to follow.

Best serif fonts (from bamag.com): Garamond (a common font), Caslon (apparently best for books), Stone, Jaslon. I don't really like serif but sometimes there is no choice.

Best for the web: Verdana, it's common enough (unlike, say, Century Schoolbook, which I also like), and it looks nicer than Arial/Helvetica.

Best sans-serif: Apple knows a lot about nice fonts, so I figure I will copy them. They use Myriad for packaging/ads etc, and it's exceptionally nice. They also use Helvetica Neue sometimes. Finally, Lucida Grande is the "OS X font".

Bioinformatics blog

2005-10-13T19:48:00.000-07:00

I stumbled upon this bioinformatics/genomics blog.
http://www.ghastlyfop.com/blog/

The 2005 zeitgeist is particularly interesting, it has a graph of hot topics (including machine learning methods) over the past year...
http://www.ghastlyfop.com/blog/2005/10/bioinformatics-zeitgeist-05.html

Web Tools

2005-10-10T18:46:00.000-07:00

Two useful sets of tools for playing with websites...

www.dnsstuff.com

www.faganfinder.com/urlinfo

God Created the Integer

2005-10-07T09:34:00.000-07:00

Check out this new book by Steven Hawkings:

God Created the Integer

Einstein and Models

2005-10-05T00:03:00.000-07:00

Here's a neat snippet about Einstein from the KQED web site:

In 1905, Albert Einstein was a pleasant but unimpressive young man in a patent office until he drafted his Theory of Relativity. Shortly thereafter he wrote a supplement saying, "The idea is amusing and enticing, but whether the Lord is laughing at it and has played a trick on me -- that I cannot know."

Nanotube RAM

2005-10-04T23:25:00.000-07:00

Check out this blurb from Nature news:

http://www.nature.com/news/2005/051003/full/051003-4.html

It seems to have real potential for providing fast, nonvolatile RAM. The company claims it will have its first products out by next year...

I'm In

2005-10-04T23:17:00.000-07:00

A quick test post to see if I'm really in... ;-D

PhD laws

2005-10-01T13:28:00.000-07:00

If you are doing a PhD, you should be aware of Hofstadter's law, and Parkinson's law. Parkinson's law comes from a very interesting book by Parkinson about the civil service.

Selenium

2005-09-26T20:41:00.000-07:00

If it's good enough for Brad Efron (he of bootstrap fame), maybe I should be taking Selenium too...

"""
Dr. Brad Efron, a professor of statistics at Stanford, has a different dietary approach. He does not have prostate cancer, but he had a couple of scares and he has friends who have it. So he is taking selenium, a trace mineral found in plants.

A study that randomly assigned people to take selenium or not to see whether it protected against skin cancer found that it had no effect on that cancer, but that the men taking it had only a third as many prostate cancers.
"""

from this NYT article on cancer and diet: Here

Top ten most cited works from 1976-1983 (via Metafilter)

2005-09-23T14:23:00.000-07:00

Nice. I have read all of these and find their ideas intriguing if simple-minded.

1. T.S. Kuhn, The Structure of Scientific Revolutions. 1962
2. J. Joyce, Ulysses. 1922
3. N. Frye, Anatomy of Criticism: Four Essays. 1957
4. L. Wittgenstein, Philosophical Investigations
5. N. Chomsky, Aspects of the Theory of Syntax. 1965
6. M. Foucault, The Order of Things. 1966
7. J. Derrida, Of Grammatology
8. R. Barthes, S/Z. 1970
9. M. Heidegger, Being and Time. 1927
10. E.R. Curtius, European Literature and the Latin Middle Ages. 1948

Another Stanford MacArthur genius

2005-09-20T10:54:00.000-07:00

Pehr Harbury of the Biochemistry Department. Last year, Daphne Koller and Julie Theriot were among the winners.

link

Humanities sucks.

2005-09-13T08:57:00.000-07:00

Nice piece in the guardian about science communication. He'll really
make friends at the Guardian with lines like:

"humanities graduates in the media, who suspect themselves to be
intellectuals, desperately need to reinforce the idea that science is
nonsense: because they've denied themselves access to the most
significant developments in the history of western thought for 200
years, and secretly, deep down, they're angry with themselves over
that."

Here

Practice Blackjack

2005-09-12T16:42:00.000-07:00

As I was exploring the potential of Javascript/DHTML in informatics-related applications, I stumbled onto another area where that technology can be put to good use -- gambling! So to practice my Javascript skills and to help beginner to intermediate Blackjack players everywhere, I wrote a small application and put it up at blackjack-bst.com (which stands for Blackjack Basic Strategy Trainer dot com). Check it out and tell me what you think. It is still a work in progress.

PLOS Clinical Trials

2005-08-29T00:11:00.000-07:00

Yup, another PLOS journal! Coming later this year, sounds cool.

Sean Eddy is moving to Janelia Farm

2005-08-16T12:44:00.000-07:00

I have not heard of that place until today but it sounds pretty amazing. [link]

Synthetic biology news from boing boing

2005-06-29T12:00:00.000-07:00

http://www.boingboing.net/2005/06/29/craig_venters_new_co.html

tinyproxy

2005-06-09T20:01:00.000-07:00

Tinyproxy is a cool little program that allows you to use your linux/mac box as a proxy with little overhead. This is useful because when you are away, say in Europe, you can access all the Stanford-accessible journals by going through your Stanford box. Like a lot of these little tools, this was introduced to me by Mike.
Tinyproxy

Freecell

2005-06-09T19:59:00.000-07:00

Javascript / DHTML are important technologies in bioinformatics. I swear that is why I did this.
Just Freecell

Synergy

2005-06-08T12:33:00.000-07:00

I've just started using Synergy. Now I can use the PC on the desk next to me (I use a Mac), with the same keyboard and mouse. All I have to do is move the mouse off the left hand side of the screen and into the PCs monitor, and I can control it! It's totally like magic.

The winbutton

2005-06-08T12:31:00.000-07:00

The BMI program has gone commercial! You the button click, money you might win. winbutton

Emacs desktop

2005-05-06T10:52:00.000-07:00

I recently found out about Emacs desktop. It's sweet. Every time you load emacs it remembers all the files you had open and automatically loads them all. Kind of like screen.

To use it you just have to add this to your .emacs.
(load "desktop")
(desktop-load-default)
(desktop-read)

Wired article

2005-05-05T15:12:00.000-07:00

There's a wired article on the fifty hippest companies. It makes for interesting reading.
http://www.wired.com/wired/archive/13.05/wired40.html

35. GEN-PROBE
A Germ's Worst Nightmare
Last year: 33
Someday doctors will use genomic data to prevent infectious diseases. Until then, there's Gen-Probe, whose nucleic acid tests detect scourges like hepatitis, HIV, pneumonia, and tuberculosis. Forty Gen-Probe products have gained FDA approval; its Procleix assay now screens more than 80 percent of the US blood supply. The result is fewer blood-borne infections, not to mention 2004 sales of $270 million and gross margins of 78 percent. That's one healthy business.
Challenge: Keep its big partners happy. Gen-Probe has been embroiled in contractual disputes with two, Chiron and Bayer.
Opportunity: Developing nations, where 43 percent of blood donations aren't tested for disease.

Using the bioxcluster

2005-05-05T13:46:00.000-07:00

Some info on the bioxcluster:

To open the firewall, eg #usernum=152, #sunetid=brian
ssh -p 259 user#usernum:skey@bioxcluster.stanford.edu
To ssh in there:
ssh -p 1000+#usernum #sunetid@bioxcluster.stanford.edu
To scp files to the cluster:
scp -oport=1000+#usernum file #sunetid@bioxcluster.stanford.edu:./
Submitting a job:
qsub job.sh
Deleting a job:
qdel job.sh
What jobs are running:
qstat, or showq (slow)

Format of simplest job.sh:
#!/bin/bash
#PBS -l nodes=1,walltime=24:00:00
#PBS -N my_job

export tempdir=$TMPDIR # temp space on local compute node
export inputdir=$HOME/dir1 # location of input files
export outputdir=$HOME/dir2 # location to put results into
export output=outfile # file for redirected standard output
export error=errfile # file for redirected standard error

cp -r $inputdir/* $tempdir

cd $tempdir

python run_program.py 1>$output 2>$error

cp outfile errfile $outputdir

Google Scholar

2005-04-28T13:35:00.000-07:00

On the Lane library web-page:

Link from Google Scholar to FindIt@Stanford

You now can set preferences in Google Scholar to show "Find It @ Stanford Med" links, which connect you to Lane's online journals. This is the equivalent of the Stanford button in PubMed:

1) Connect to Google Scholar.

2) Click on Scholar Preferences to the right of the search box.

3) Check the box "Stanford University Medical Center (Find It @ Stanford Med)"

4) Click the Save Preferences button and continue searching.

5) Look for links in your search results labeled Find It @ Stanford Med Note that when on campus, you will also see links to "Find It @ Stanford" -- this version is provided by the main campus library system.

Inteins

2005-04-27T19:03:00.000-07:00

What are inteins? Doug mentioned them to me today, and I had never heard of them. The short answer is that they are like introns, but in proteins. They splice themselves out of their host protein, and they only exist in single celled organisms, AFAIK. I think this pretty much means we have seen everything possible happen in biology now, bar reverse translation, which I am still not convinced does not exist. I can't find any really good reviews, but this paper is OK.
http://www.pubmedcentral.gov/articlerender.fcgi?tool=pmcentrez&artid=23508

Useful Python functions

2005-04-15T14:35:00.000-07:00

Recently, I have been using these functions a lot. Maybe they will be of use to others.
These functions:

sort a list of objects by an attribute, eg sort_by_attr(people, 'name')
sort a list of objects by a list of attributes eg sort_by_attrs(people, ['lastname','firstname']
print out all of the attributes of an object.

Read more

In the bleak bleak perl days, I might have made a list of blast hits as a dictionary of dictionaries, eg hit[gene1][gene2] = 10. Of course it's much neater to do it like this
hit = Container()
hit.gene1 = gene1
hit.gene2 = gene2
hit.score = score
Then you can sort by score, gene1, gene2 etc etc..


def sort_by_attr(seq,attr):
  """stably sort by an attribute"""
  seq2 = [[getattr(s,attr),i,s] for i,s in enumerate(seq)]
  seq2.sort()
  return [s[2] for s in seq2]

def sort_by_attr_inplace(seq,attr):
  """stably sort by an attribute in place"""
  seq[:] = sort_by_attr(seq,attr)

def sort_by_attrs(seq,attrs):
  """sort by a few attributes"""
  import copy
  seq2 = copy.copy(seq)
  attrs.reverse()
  for attr in attrs:
    seq2 = sort_by_attr(seq2,attr)

 return seq2

def sort_by_attrs_inplace(seq,attrs):
  """sort by a few attributes in place"""
  attrs.reverse()
  for attr in attrs:
    seq[:] = sort_by_attr(seq,attr)


def print_all_attrs(obj_instance):
  attrs = dir(obj_instance)
  for attr in attrs:
    if attr[:2] == '__':
       continue
    print attr, getattr(obj_instance,attr)

Innocentive

2005-04-11T13:04:00.000-07:00

This seems like an efficient way to do science. Makes sense in a free-market kind of way. Here is the accompanying Scientist article (Stanford accessible only).

Stanford informatics in South Africa

2005-04-11T12:49:00.000-07:00

Here is a short article on Stanford's informatics collaboration in South Africa. You can use no@no.com to view genomeweb articles.

More Beauracracy, Please

2005-04-09T08:44:00.000-07:00

How fast can the government respond to scientific studies? Pretty fast, it seems. On page 178 in this week's Science, the results of a large survey of the nation's postdocs is published. One of the conclusions of the study: What really counts is not the money but the [postdoc] experience.

It appears that the government has taken that to heart. The next story (on the same page): IRS Takes Bite out of NIH Fellows' Paychecks. Almost 5000 postoctoral scholars supported by NIH fellowships took a 7.65% pay cut this week...

for sale: blog

2005-04-07T15:45:00.000-07:00

Anyone want to buy the bmi students blog? It's cheap at half the price.

best papers of 2004

2005-04-05T11:55:00.000-07:00

My friend sent me a list of papers, voted best of the year by his lab.
Read more

Jordan IK, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV,
Kondrashov AS, Sunyaev S. A universal trend of amino acid gain and
loss in protein evolution. Nature. 2005 Feb 10;433(7026):633-8. Epub
2005 Jan 1 abstract

here

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen
JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH,
Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R,
Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental
genome shotgun sequencing of the Sargasso Sea. Science. 2004 Apr
2;304(5667):66-74. Epub 2004 Mar 4. abstract
here

Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL,
Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global
identification of human transcribed sequences with genome tiling
arrays. Science. 2004 Dec 24;306(5705):2242-6. Epub 2004 Nov 11.
abstract
here

Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE, Lamond AI, Mann M.
Nucleolar proteome dynamics. Nature. 2005 Jan 6;433(7021):77-83.
abstract
here

Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B. JASPAR:
an open-access database for eukaryotic transcription factor binding
profiles. Nucleic Acids Res. 2004 Jan 1;32(Database issue)D91-4.
abstract
here

Ramachandran N, Hainsworth E, Bhullar B, Eisenstein S, Rosen B, Lau
AY, Walter JC, LaBaer J. Self-assembling protein microarrays.
Science. 2004 Jul 2;305(5680):86-90. abstract
here

Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith
SF, North P, Callaway H, Kelly K, Walter K, Abnizova I, Gilks W,
Edwards YJ, Cooke JE, Elgar G. Highly conserved non-coding sequences
are associated with vertebrate development. PLoS Biol. 2005
Jan;3(1):e7. Epub 2004 Nov 1 abstract
here

Gerber AP, Herschlag D, Brown PO. Extensive association of
functionally and cytotopically related mRNAs with Puf family
RNA-binding proteins in yeast. PLoS Biol. 2004 Mar;2(3):E79. Epub
2004 Mar 16. abstract
here

Brown P, Sutikna T, Morwood MJ, Soejono RP, Jatmiko, Saptomo EW, Due
RA. A new small-bodied hominin from the Late Pleistocene of Flores,
Indonesia. Nature. 2004 Oct 28;431(7012):1055-61 abstract
here

Wang C, Lefkowitz EJ. SS-Wrapper: a package of wrapper applications
for similarity searches on Linux clusters. BMC Bioinformatics. 2004
Oct 28;5(1):171. abstract
here

Dwyer MA, Looger LL, Hellinga HW. Computational design of a
biologically active enzyme. Science. 2004 Jun 25;304(5679):1967-71.
abstract
here

Aharoni A, Gaidukov L, Khersonsky O, McQ Gould S, Roodveldt C,
Tawfik DS. The 'evolvability' of promiscuous protein functions. Nat
Genet. 2005 Jan;37(1):73-6. Epub 2004 Nov 28 abstract
here

Segal E, Friedman N, Koller D, Regev A. A module map showing
conditional activity of expression modules in cancer. Nat Genet.
2004 Oct;36(10):1090-8. Epub 2004 Sep 26. abstract
here

Park JW, Parisky K, Celotto AM, Reenan RA, Graveley BR.
Identification of alternative splicing eegulators by RNA
interference in Drosophila. Proc Natl Acad Sci U S A. 2004 Nov
9;101(45):15974-9. Epub 004 Oct 18. abstract
here

Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola
B, Suzan M, Claverie JM. The 1.2-megabase genome sequence of
Mimivirus. Science. 2004 Nov 19;306(5700):1344-50. Epub 2004 Oct 14.
abstract
here

King RD, Whelan KE, Jones FM, Reiser PG, Bryant CH, Muggleton SH,
Kell DB, Oliver SG. Functional genomic hypothesis generation and
experimentation by a robot scientist. Nature. 2004 Jan
5;427(6971):247-52. abstract
here

add bmistudents to my yahoo

2005-03-25T21:15:00.000-08:00

Go to my.yahoo.com
Sign in and click on add content
Click on add rss by url
Add the following url:
http://bmistudents.blogspot.com/atom.xml
Click on add.

Now you can read it on your my.yahoo.com page.

Blogs are good?

2005-03-25T12:42:00.000-08:00

Artificial organs validates the blog.

RNAi

2005-03-25T10:23:00.000-08:00

To me, RNAi was always a confusing mess of different biochemical processes. This animation brings it all into sharp relief. I can't stress how sweet it is.

Journals

2005-03-24T23:39:00.000-08:00

What are the most awesome journals? My favourites are Nature [Reviews] Genetics, Trends in Genetics, and Genome Research. Genome Biology also seems to have good data-set papers. I don't know many people that read Trends X, but those journals have a lot of great reviews on cutting edge science. Diane mentioned Bioessays to as being a good one, and I quite like it, though I have to go through Lane library's eJournals to get it for some reason.

Impression of Job Talks

2005-03-24T15:46:00.000-08:00

I've been attending the faculty candidate talks that the Radiology department has been having. First off, many have been very they're interesting talks. A second benefit is that attending these talks is a chance to see lots of people give job talks, and to see what works and what does not.

Here are some very subjective (and likely incorrect) ideas I've had about what works and what doesn't work.

First, it seems important to actually have poeple in attendance at the talk. This is probably all showmanship, but it seems that the more people are there, the more exciting the talk seems and the better the questions you get. If I were giving a job talk, I'd try to ensure that friends and friends of friends were in attendance.

Next, the more successful talks all seemed to be somewhat tailored to the specific interests of the department. Some talks seemed generic, and some seemed like they'd been customized to appeal to whatever it was that the search committee was looking for. I don't need to tell you which ones appeared better. Also, make sure the level of detail -- and choice of details -- is appropriate: talks that were CS-theory-heavy when the audience was mostly radiologists? No good. Talks that spent minutes on the central dogma for the same audience? No better.

Also, more successful talks were "multi-scale" -- that is, they covered a "big picture" of a very exciting area, then gave detailed results about work that clearly has implications on the "big picture." The best talks also included a section on potential research approaches that the candidate would presumably do if they got the job. This section, in my opinion, should be the bridge between the small-scale research results and the big picture. The point here being that you appear to be (a) a visionary, (b) able to do real reasearch, and (c) able to connect real research to a vision of what you want to do.

I liked talks that showed how the person in question had a particular set of skills exactly appropriate for what they wanted to do. Nothing blatant, of course! But talks that gave the listener the impression that the speaker had the "perfect training" to do whatever made the speaker seem to be a very good candidate.

If any of you saw Atul's job talk, I think that's an example of one that hit all of these criteria.

Writing python extensions in C++

2005-03-19T11:22:00.000-08:00

I love Python. However, as of late, I have also come to understand why C++ can be a very useful language too. So I've been trying to find good ways of calling my C++ code from Python. The standard routes are to either use SWIG or write an extension in C.

SWIG is great and usually simple, but sometimes can feel too inflexible. Writing C extensions is super-flexible, but requires a lot of boilerplate code to do it correctly.

Today I found PyCXX, which is a set of C++ classes which work like C++ STL types, but proxy to Python objects. Now it's dead simple to integrate my C++ code with my Python code and have everything (a) work well, and (b) look nice.

Here's an example of manipulating a Python dictionary in Python:
d = {} d["a"] = 1 d["b"] = 2 alist = d.keys() print alist
And the same example in C++ with PyCXX:
Dict d; List alist; d["a"] = Int(1); d["b"] = Int(2); alist = d.keys(); std::cout << alist << std::endl;

Notice how easy it is to use Python objects in your C++ code?