Mailman 3 May 2012 - SciPy-User

2012 SciPy Bioinformatics Workshop
by Chris Mueller 03 May '12

03 May '12

We are pleased to announce the 2012 SciPy Bioinformatics Workshop held in conjunction with SciPy 2012 this July in Austin, TX. Python in biology is not dead yet... in fact, it's alive and well! Remember just a few short years ago when BioPerl ruled the world? Just one minor paradigm shift* later and Python now has a commanding presence in bioinformatics. From Python bindings to common tools all the way to entire Python-based informatics platforms, Python is used everywhere** in modern bioinformatics. If you use Python for bioinformatics or just want to learn more about how its being used, join us at the 2012 SciPy Bioinformatics Workshop. We will have speakers from both academia and industry showcasing how Python is enabling biologists to effectively work with large, complex data sets. The workshop will be held the evening of July 19 from 5-6:30. More information about SciPy is available on the conference site: http://conference.scipy.org/scipy2012/ !! Participate !! Are you using Python in bioinformatics? We'd love to have you share your story. We are looking for 3-4 speakers to share their experiences using Python for bioinformatics. Please contact Chris Mueller at chris.mueller [at] lab7.io and Ray Roberts at rroberts [at] enthought.com to volunteer. Please include a brief description or link to a paper/topic which you would like to discuss. Presentations will last for 15 minutes each and will be followed by a panel Q&A. -- * That would be next generation sequencing ** Yes, we aRe awaRe of that otheR language used eveRywhere, but let's celebRate Python Right now.

1 0

Least-square fitting of a 3rd degree polynomial
by camille chambon 02 May '12

02 May '12

Hello, I would like to fit 'a' such as y = a * x**3 + b * x**2 + c * x + d, where x and y are measured data, and b = 0.0, c = -0.00458844157413 and d = 5.8 are fixed. According to http://www.scipy.org/Cookbook/FittingData#head-27373a786baa162a2e8a910ee0b8…, I try to use scipy.optimize.leastsq fit routine like that: #### CODE ##### from numpy import * from pylab import * from scipy import optimize # My data points x = array([1078.0, 1117.0, 1212.1, 1368.7, 1686.8, 1880.0]) y = array([5.8, 5.6, 5.4, 4.9, 2.4, 0.0]) b, c, d = 0.0, -0.00458844157413, 5.8 # Fixed parameters fitfunc = lambda p, x: poly1d([p[0], b, c, d])(x) # Target function errfunc = lambda p, x, y: fitfunc(p, x) - y # Distance to the target function p0 = [-4.0E-09] # Initial guess for the parameters p1, success = optimize.leastsq(errfunc, p0[:], args=(x, y)) time = linspace(x.min(), x.max(), 100) plot(x, y, "ro", time, fitfunc(p1, time), "r-") # Plot of the data and the fit title("a fitting") xlabel("time [day]") ylabel("number []") legend(('x position', 'x fit', 'y position', 'y fit')) show() ################################ But the fit does not work (as one can see on the attached image). Does someone have any idea of what I'm doing wrong? Thanks in advance for your help. Cheers, Camille

3 8

building on Ubuntu Linux from github source : BLAS and LAPACK not getting picked up from environment variable
by hari jayaram 01 May '12

01 May '12

Hi I am on 64 bit Ubuntu , python 2.6.5 , GCC 4.4.3. I want to compile my own scipy since the ubuntu package on lucid installs a scipy which does not have the scipy.optimize.curve_fit I followed the build instructions at the url below to install from the git source . http://www.scipy.org/Installing_SciPy/BuildingGeneral I could install numpy from the git source . Then I installed lapack and blas libraries in my home directory following the instructions at BuildingGeneral. I set the environment variables BLAS and LAPACK in my ~/.bashrc and sourced them and then tried the setup.py for scipy sudo python setup.py install I get the following errors implying that BLAS was not getting picked up. I even copied the libblas.a and liblapack.a files to /usr/lib, linked it to liblapack.so ...but none of these helped find lapack or blas "numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable." I am wondering if the build instructions are different for the github tree. The detailed error is given below. Thanks for your help Hari hari@hari:~/scipy$ sudo python setup.py install --prefix=/usr/local blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1474: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1483: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1486: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last): File "setup.py", line 208, in <module> setup_package() File "setup.py", line 199, in setup_package configuration=configuration ) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 136, in configuration config.add_subpackage('scipy') File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 8, in configuration config.add_subpackage('integrate') File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/integrate/setup.py", line 10, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py", line 325, in get_info return cl().get_info(notfound_action) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py", line 484, in get_info raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. hari@hari:~/scipy$ export BLAS=/home/hari/blas/BLAS/libblas.a hari@hari:~/scipy$ export LAPACK=/home/hari/LAPACK/lapack-3.4.0/liblapack.a hari@hari:~/scipy$ sudo python setup.py install --prefix=/usr/local blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1474: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) blas_info: libraries blas not found in ['/usr/local/lib', '/usr/lib64', '/usr/lib'] NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1483: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) blas_src_info: NOT AVAILABLE /usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py:1486: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last): File "setup.py", line 208, in <module> setup_package() File "setup.py", line 199, in setup_package configuration=configuration ) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 136, in configuration config.add_subpackage('scipy') File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 8, in configuration config.add_subpackage('integrate') File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/integrate/setup.py", line 10, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py", line 325, in get_info return cl().get_info(notfound_action) File "/usr/local/lib/python2.6/dist-packages/numpy/distutils/system_info.py", line 484, in get_info raise self.notfounderror(self.notfounderror.__doc__) numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable.

2 2

SciPy 2012 Abstract and Tutorial Deadlines Extended
by Warren Weckesser 30 Apr '12

30 Apr '12

SciPy 2012 Conference Deadlines Extended Didn't quite finish your abstract or tutorial yet? Good news: the SciPy 2012 organizers have extended the deadline until Friday, May 4. Proposals for tutorials and abstracts for talks and posters are now due by midnight (Austin time, CDT), May 4. For the many of you who have already submitted an abstract or tutorial: thanks! If you need to make corrections to an abstract or tutorial that you have already submitted, you may resubmit it by the same deadline. The SciPy 2012 Organizers

1 0