Skip to main content

SAGEMATH : Open source and a good alternative to Mathematica, Maple, Matlab, Magma

SAGEMATH
It is an open source Mathematics software created by people who use it everyday. It is developed by mathematician doing research in math at universities. It is good because it is totally free, not like Mathematica which is expensive and closed source. Closed source means you don't have an idea of their working and you can not modify them. As Mathematica is very expensive, it is a real issues for the universities and for the developing countries to buy their licenses and install to teach to the students or to use it in research. No doubt SAGEMATH is playing a huge role in this aspect and that's the reason SAGEMATH is rapidly expanding.

Download:
http://www.sagemath.org/download.html

Installation of SAGEMATH:
Please follow the following links for the installation.
http://doc.sagemath.org/html/en/installation/

Several packages has been installed during SAGEMATH installation.
alabaster-0.7.12.tar.gz
appnope-0.1.0.tar.gz
arb-2.16.0.tar.gz
Babel-2.6.0.tar.gz
backports_abc-0.5.tar.gz
backports.functools_lru_cache-1.5.tar.gz
backports.shutil_get_terminal_size-1.0.0.tar.gz
backports_ssl_match_hostname-3.5.0.1.tar.gz
bleach-3.0.2.tar.gz
boost_cropped-1.66.0.tar.bz2
brial-1.2.4.tar.bz2
bzip2-1.0.6-20150304.tar.gz
cddlib-0.94j.tar.gz
certifi-2018.11.29.tar.gz
cliquer-1.21.tar.gz
combinatorial_designs-20140630.tar.bz2
configparser-3.5.0.tar.gz
conway_polynomials-0.5.tar.bz2
curl-7.62.0.tar.bz2
cvxopt-1.1.8.tar.gz
cycler-0.10.0.tar.gz
cypari2-2.1.0.tar.gz
cysignals-1.10.2.tar.gz
Cython-0.29.5.tar.gz
decorator-4.3.0.tar.gz
defusedxml-0.5.0.tar.gz
docutils-0.14.tar.gz
ecl-16.1.2.tar.bz2
eclib-20190226.tar.bz2
ecm-7.0.4.tar.gz
elliptic_curves-0.8.tar.bz2
entrypoints-0.2.3.tar.gz
enum34-1.1.6.tar.gz
fflas_ffpack-2.3.2.tar.bz2
Flask-0.10.1.tar.gz
Flask_AutoIndex-0.6.tar.gz
Flask_Babel-0.9.tar.gz
Flask_OldSessions-0.10.tar.gz
Flask_OpenID-1.2.5.tar.gz
Flask_Silk-0.2.tar.gz
flint-2.5.2.tar.gz
flintqs-1.0.tar.bz2
fplll-5.2.1.tar.gz
fpylll-0.4.1dev.tar.gz
freetype-2.9.1.tar.bz2
functools32-3.2.3-2.tar.gz
future-0.17.1.tar.gz
gap-4.10.0.tar.gz
gc-7.6.4.tar.gz
gcc-7.2.0.tar.xz
gf2x-1.2.tar.gz
gfan0.6.2.tar.gz
giac-1.5.0.37.tar.bz2
git-2.11.0.tar.gz
givaro-4.0.4.tar.gz
glpk-4.63.tar.bz2
gmpy2-2.1.0a4.tar.gz
graphs-20161026.tar.bz2
gsl-2.5.tar.gz
html5lib-1.0.1.tar.gz
imagesize-1.1.0.tar.gz
iml-1.0.4p1.tar.bz2
ipaddress-1.0.22.tar.gz
ipykernel-4.8.2.tar.gz
ipython-5.8.0.tar.gz
ipython_genutils-0.2.0.tar.gz
ipywidgets-7.4.2.tar.gz
itsdangerous-1.1.0.tar.gz
jinja2-2.10.tar.gz
jmol-14.6.1_2016.07.11.tar.bz2
jsonschema-2.6.0.tar.gz
jupyter_client-5.2.4.tar.gz
jupyter_core-4.4.0.tar.gz
kiwisolver-1.0.1.tar.gz
lcalc-1.23.tar.bz2
libatomic_ops-7.6.2.tar.gz
libbraiding-1.0.tar.gz
libffi-3.2.1.tar.gz
libgd-2.1.1.1.tar.bz2
libhomfly-1.02r4.tar.gz
libiconv-1.15.tar.gz
libpng-1.6.29.tar.gz
linbox-1.5.2.tar.gz
lrcalc-1.2.tar.gz
m4ri-20140914.tar.gz
m4rie-20150908.tar.gz
markupsafe-1.1.0.tar.gz
mathjax-2.7.4.tar.gz
matplotlib-2.2.3.tar.bz2
maxima-5.41.0.tar.gz
mistune-0.8.4.tar.gz
mpc-1.1.0.tar.gz
mpfi-1.5.2.tar.bz2
mpfr-4.0.1.tar.bz2
mpir-3.0.0-644faf502c56f97d9accd301965fc57d6ec70868.tar.bz2
mpmath-1.1.0.tar.gz
nauty-26r1.tar.gz
nbconvert-5.4.0.tar.gz
nbformat-4.4.0.tar.gz
ncurses-6.0.tar.gz
networkx-2.2.zip
nose-1.3.7.tar.gz
notebook-5.7.6.tar.gz
ntl-10.3.0.tar.gz
numpy-1.16.1.zip
openblas-0.3.5.tar.gz
packaging-18.0.tar.gz
palp-2.1.tar.bz2
pandocfilters-1.4.2.tar.gz
pari-2.11.1.tar.gz
pari_galdata-20080411.tar.bz2
pari_seadata_small-20090618.tar.bz2
patch-2.7.5.tar.gz
pathlib2-2.3.3.tar.gz
pathpy-7.1.tar.bz2
pcre-8.40.tar.gz
pexpect-4.6.0.tar.gz
pickleshare-0.7.5.tar.gz
Pillow-5.3.0.tar.gz
pip-18.1.tar.gz
pkgconf-0.9.7.tar.gz
pkgconfig-1.4.0.tar.gz
planarity-3.0.0.5.tar.gz
polytopes_db-20170220.tar.bz2
ppl-1.2.tar.bz2
pplpy-0.8.4.tar.gz
prometheus_client-0.5.0.tar.gz
prompt_toolkit-1.0.15.tar.gz
psutil-5.2.0.tar.gz
ptyprocess-0.5.1.tar.gz
PyCygwin-0.1.tar.gz
Pygments-2.3.1.tar.gz
pynac-0.7.24.tar.bz2
pyparsing-2.3.0.tar.gz
Python-2.7.15.tar.xz
Python-3.6.6.tar.gz
python-dateutil-2.5.3.tar.gz
python_openid-2.2.5.tar.gz
pytz-2018.7.tar.bz2
pyzmq-17.1.2.tar.gz
R-3.5.2.tar.gz
ratpoints-2.1.3.tar.bz2
readline-6.3.008.tar.gz
requests-2.13.0.tar.gz
rpy2-2.8.2.tar.gz
rubiks-20070912.tar.bz2
rw-0.7.tar.gz
sagenb-1.1.2.tar.bz2
sagenb_export-3.2.tar.gz
sagetex-3.2.tar.gz
scandir-1.9.0.tar.gz
scipy-1.2.0.tar.gz
Send2Trash-1.5.0.tar.gz
setuptools-40.6.3.zip
setuptools_scm-3.1.0.tar.gz
simplegeneric-0.8.1.tar.bz2
singledispatch-3.4.0.3.tar.gz
singular-4.1.1p2.tar.gz
six-1.12.0.tar.gz
snowballstemmer-1.2.1.tar.gz
speaklater-1.3.tar.gz
Sphinx-1.7.6.tar.gz
sphinxcontrib-websupport-1.1.0.tar.gz
sqlite-autoconf-3270100.tar.gz
subprocess32-3.5.3.tar.gz
symmetrica-2.0.tar.bz2
sympow-1.018.1.tar.bz2
sympy-1.3.tar.gz
tachyon-0.98.9.tar.bz2
terminado-0.8.1.tar.gz
testpath-0.4.2.tar.gz
thebe-9624e0a0.zip
threejs-r80.tar.gz
tornado-4.5.2.tar.gz
traitlets-4.3.2.tar.gz
Twisted-16.3.0.tar.bz2
typing-3.6.6.tar.gz
vcversioner-2.16.0.0.tar.gz
wcwidth-0.1.7.tar.gz
webencodings-0.5.1.tar.gz
Werkzeug-0.14.1.tar.gz
widgetsnbextension-3.4.2.tar.gz
xz-5.2.2.tar.gz
yasm-1.3.0.tar.gz
zeromq-4.2.5.tar.gz
zlib-1.2.11.tar.gz
zn_poly-0.9.1.tar.gz
zope.interface-4.6.0.tar.gz


4ti2                                mercurial
alabaster                           mistune
appnope                             modular_decomposition
arb                                 mpc
atlas                               mpfi
autotools                           mpfr
babel                               mpfrcx
backports_abc                       mpi4py
backports_functools_lru_cache       mpir
backports_shutil_get_terminal_size  mpmath
backports_ssl_match_hostname        nauty
barvinok                            nbconvert
beautifulsoup                       nbformat
benzene                             ncurses
biopython                           networkx
bleach                              nibabel
bliss                               ninja_build
boost                               normaliz
boost_cropped                       nose
brial                               notebook
brian                               notedown
buckygen                            ntl
bzip2                               numpy
cbc                                 openblas
ccache                              openssl
cddlib                              ore_algebra
certifi                             packaging
cliquer                             palp
cmake                               pandoc_attributes
cocoalib                            pandocfilters
combinatorial_designs               pari
compilerwrapper                     pari_elldata
configparser                        pari_galdata
configure                           pari_galpol
conway_polynomials                  pari_jupyter
coxeter3                            pari_nftables
cryptominisat                       pari_seadata
csdp                                pari_seadata_small
curl                                patch
cvxopt                              pathlib2
cycler                              pathpy
cypari                              pcre
cysignals                           perl_term_readline_gnu
cython                              pexpect
d3js                                p_group_cohomology
database_cremona_ellcurve           pickleshare
database_jones_numfield             pillow
database_kohel                      pip
database_mutation_class             pkgconf
database_odlyzko_zeta               pkgconfig
database_stein_watkins              planarity
database_stein_watkins_mini         plantri
database_symbolic_data              polylib
dateutil                            polymake
decorator                           polytopes_db
deformation                         ppl
defusedxml                          pplpy
docutils                            primecount
dot2tex                             prometheus_client
ecl                                 prompt_toolkit
eclib                               psutil
ecm                                 ptyprocess
elliptic_curves                     pybtex
entrypoints                         pycosat
enum34                              pycygwin
fflas_ffpack                        pyflakes
flask                               pygments
flask_autoindex                     pynac
flask_babel                         pynormaliz
flask_oldsessions                   pyopenssl
flask_openid                        pyparsing
flask_silk                          pysingular
flint                               python2
flintqs                             python3
fplll                               python_igraph
fpylll                              python_openid
freetype                            pytz
fricas                              pyx
frobby                              pyzmq
functools32                         qepcad
future                              qhull
gambit                              r
gap                                 ratpoints
gap3                                readline
gap_jupyter                         requests
gap_packages                        r_jupyter
gc                                  rpy2
gcc                                 rst2ipynb
gdb                                 rubiks
gf2x                                rw
gfan                                saclib
gfortran                            sagenb
giac                                sagenb_export
giacpy_sage                         sagetex
git                                 scandir
git_trac                            scipoptsuite
givaro                              scipy
glpk                                scons
glucose                             send2trash
gmp                                 setuptools
gmpy2                               setuptools_scm
gp2c                                simplegeneric
graphs                              singledispatch
gsl                                 singular
guppy                               singular_jupyter
html5lib                            sip
iconv                               sirocco
igraph                              six
imagesize                           snowballstemmer
iml                                 speaklater
ipaddress                           sphinx
ipykernel                           sphinxcontrib_websupport
ipython                             sqlalchemy
ipython_genutils                    sqlite
ipywidgets                          subprocess32
isl                                 surf
itsdangerous                        symmetrica
jinja2                              sympow
jmol                                sympy
jsonschema                          tachyon
jupyter_client                      tdlib
jupyter_core                        termcap
kenzo                               terminado
kiwisolver                          testpath
latte_int                           texlive
lcalc                               thebe
libatomic_ops                       threejs
libbraiding                         tides
libffi                              topcom
libgd                               tornado
libhomfly                           trac
libogg                              traitlets
libpng                              twisted
libtheora                           typing
lidia                               valgrind
lie                                 vcversioner
linbox                              wcwidth
lrcalc                              webencodings
lrslib                              werkzeug
m4ri                                widgetsnbextension
m4rie                               xz
markupsafe                          yasm
mathjax                             zeromq
matplotlib                          zlib
maxima                              zn_poly
mcqd                                zope_interface

Comments

Most Viewed Post

How to keep chain ID / IDs in GROMACS?

In GROMACS , while converting pdb file (monomer or multimer) into .gro file, it do not preserve the chain ID information. Due to the lack of chain ID information, pdb file retrieved from .gro file at any stage of the simulation has missing chain IDs and pdb file can not be visualized properly in PYMOL / RASMOL . There are two ways to convert .gro file into .pdb Lets say your protein name is xyz.pdb 1] gmx editconf -f xyz.gro -o xyz.pdb 2] gmx trjconv -f  xyz.gro -o xyz.pdb -s xyz.tpr Only ' trjconv ' will retrieve the chain ID information for all the chains. and not ' editconf '. If you have monomer protein and wish to assign any chain ID then following command will be of your interest: gmx editconf -f xyz.gro -o xyz.pdb -label [ chain-ID ]

GNUPLOT: How to draw trend line?

How to draw trend line in the GNUPLOT? If you like to plot graphs in gnuplot and dont know how to plot trendline then here you are. Follow the steps mentioned below... 1. You should have a files with X and Y values 2. Open GNUPLOT (Operating system dosen't change anything here. It works on all systems) 3. Type the command in the gnuplot terminal Lets say I have a file for eg. '1.txt' p '1.txt' u 1:2 w d title '', '1.txt' u 1:2 smooth acsplines title '1.txt' OR p '1.txt' u 1:2 w d title '', '1.txt' u 1:2 smooth bezier title '1.txt' It will plot as below...

MD convert (xtc to dcd)

CATDCD program can be used to convert one file format to another file format. For example: How to convert trajectory output of GROMACS .xtc format into NAMD .dcd format ==== /path/to/catdcd -o /path/to/save/file/abc.dcd -xtc /input/path/to/save/file/abc.xtc ==== How to install CATDCD? Follow the link-   https://www.ks.uiuc.edu/Development/MDTools/catdcd/ Download the catdcd-X.Xx.tar.gz Extract all files from the tar. Locate the catdcd file. It should be in directory :  catdcd-4.0b/LINUXAMD64/bin/catdcd4.0/ Source the catdcd in your bashrc: export PATH="/path/to/catdcd/directory/:$PATH"

Python : Turtle tree

Turtle module can be used to draw some very nice patterns in Python. Following are some examples with code. ==================== import turtle import random t = turtle.Turtle( shape = "circle" ) t.lt( 90 ) lv = 14 l = 120 s = 30 t.color( 'indigo' ) t.width(lv) t.penup() t.bk(l) t.pendown() t.fd(l) def draw_tree ( l , level ): width = t.width() # save the current pen width t.width(width * 3.0 / 4.0 ) # narrow the pen width l = 3.0 / 4.0 * l #t.color(R,G,B) #provide the RGB numbers t.color(random.random(), random.random(), random.random()) t.lt(s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.rt( 2 * s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.lt(s) t.width(width) # restore the previous pen width t.speed( "fastest" ) draw_tree(l, 5 ) turtle.done() ===========

USA COVID Tracking state-level COVID-19 case testing data

 

Science News

Enter your email address:

PhD Vacancy Bioinformatics

PhD Vacancy Chemoinformatics