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1Kerko
Bibliography frontend for Zotero bibs. Python, Flask.
9 months ago by @filologanoga
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bibliography
python
software
bibliographypythonsoftware
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1POSS-UniMe/simple-physics-with-Python
https://github.com/POSS-UniMe/simple-physics-with-Python/tree/main
a year ago by @johb
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jupyter
physics
python
software
tools
jupyterphysicspythonsoftwaretools
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2Home page for the PyPDF2 project
http://mstamy2.github.io/PyPDF2/
3 years ago by @ubt.rohlfs
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pdf
python
software
textsatz
pdfpythonsoftwaretextsatz
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1pymethylprocess · PyPI
Preprocessing methylation pipeline, written in python. Easy to use and highly parallelized.
4 years ago by @marcsaric
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cancer-research
methylation
python
software
cancer-researchmethylationpythonsoftware
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1openvax/varcode: Library for manipulating genomic variants and predicting their effects
Library for manipulating genomic variants and predicting their effects - openvax/varcode
4 years ago by @marcsaric
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python
software
variant-annotation
pythonsoftwarevariant-annotation
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1ABlog for Sphinx — ABlog
ABlog is a Sphinx extension that converts any documentation or personal website project into a full-fledged blog with:
4 years ago by @mjbrown
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blog
documenting
python
software
static
tools
web
blogdocumentingpythonsoftwarestatictoolsweb
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1Python - Journal of Open Source Software
https://joss.theoj.org/papers/in/Python
5 years ago by @analyst
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collection
journal
opensource
paper
programming
python
software
collectionjournalopensourcepaperprogrammingpythonsoftware
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3awesome-python: A curated list of awesome Python frameworks, libraries, software and resources
A curated list of awesome Python frameworks, libraries, software and resources - vinta/awesome-python
5 years ago by @mjbrown
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awesome
frameworks
libs
programming
python
resources
software
softwaredev
tools
awesomeframeworkslibsprogrammingpythonresourcessoftwaresoftwaredevtools
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2Python For Beginners | Python.org
The official home of the Python Programming Language
5 years ago by @osso73
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software
how-to
technical
learning
python
softwarehow-totechnicallearningpython
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1The PySD Cookbook — PySD-Cookbook 0.1.0 documentation
https://pysd-cookbook.readthedocs.io/en/latest/
5 years ago by @schmidt2
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cookbook
framework
python
readthedocs
simulation
software
system_dynamics
systems_thinking
tool
cookbookframeworkpythonreadthedocssimulationsoftwaresystem_dynamicssystems_thinkingtool
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1Text-Fabric
Text-Fabric is a Python3 package for Text plus Annotations. It provides a data model, a text file format, a binary format, an API, and apps for (ancient) text plus (linguistic) annotations.
6 years ago by @avs
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Bibel
Digital_Humanities
Griechisch
Hebräisch
Python
Software
Syrisch
BibelDigital_HumanitiesGriechischHebräischPythonSoftwareSyrisch
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1SymPy
https://www.sympy.org/en/index.html
6 years ago by @chsk
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Algebra
Dokumentation
Python
Software
SymPy
SymbolischeMathematik
AlgebraDokumentationPythonSoftwareSymPySymbolischeMathematik
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1IPython Documentation — IPython 7.2.0 documentation
https://ipython.readthedocs.io/en/stable/index.html
6 years ago by @chsk
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Dokumentation
IPython
Python
Software
DokumentationIPythonPythonSoftware
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1QuantEcon
https://quantecon.org/
6 years ago by @chsk
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Julia
Makroökonomie
Modellierung
Python
QuantEcon
Software
Ökonomie
JuliaMakroökonomieModellierungPythonQuantEconSoftwareÖkonomie
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13.7.1 Documentation
https://docs.python.org/3/index.html
6 years ago by @chsk
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Dokumentation
Python
Software
DokumentationPythonSoftware
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1reStructuredText Primer — Sphinx 2.0.0+/07b7821 documentation
http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
6 years ago by @chsk
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Dokumentation
Python
Software
Styleguide
reST
reStructuredText
DokumentationPythonSoftwareStyleguidereSTreStructuredText
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1numpydoc docstring guide — numpydoc v0.9.dev0 Manual
https://numpydoc.readthedocs.io/en/latest/format.html
6 years ago by @chsk
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Dokumentation
Python
Software
Styleguide
numpy
DokumentationPythonSoftwareStyleguidenumpy
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2PEP 8 -- Style Guide for Python Code | Python.org
https://www.python.org/dev/peps/pep-0008/
6 years ago by @chsk
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Python
Software
Styleguide
PythonSoftwareStyleguide
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4Project Jupyter | Home
https://jupyter.org/
6 years ago by @chsk
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Jupyter
Python
Software
JupyterPythonSoftware
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2Jupyter and the future of IPython — IPython
https://ipython.org/
6 years ago by @chsk
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IPython
Jupyter
Python
Software
IPythonJupyterPythonSoftware
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2Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit
N. O'Boyle, C. Morley, and G. Hutchison. Chemistry Central Journal, 2 (1): 5+ (2008)
6 years ago by @fairybasslet
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cheminformatics
open-source
openbabel
pybel
python
software
toolkit
cheminformaticsopen-sourceopenbabelpybelpythonsoftwaretoolkit
(0)
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3PyMix - The Python mixture package - a tool for clustering of heterogeneous biological data
B. Georgi, I. Costa, and A. Schliep. BMC Bioinformatics, 11 (1): 9+ (Jan 6, 2010)
6 years ago by @karthikraman
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clustering
python
software
clusteringpythonsoftware
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1MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
J. Egea, D. Henriques, T. Cokelaer, A. Villaverde, A. MacNamara, D. Danciu, J. Banga, and J. Rodriguez. BMC Bioinformatics, 15 (1): 136+ (May 10, 2014)
6 years ago by @karthikraman
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matlab
parameter-estimation
python
software
systems-biology
toolbox
matlabparameter-estimationpythonsoftwaresystems-biologytoolbox
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3IPython: A System for Interactive Scientific Computing
F. Perez, and B. Granger. Computing in Science & Engineering, 9 (3): 21--29 (May 1, 2007)
6 years ago by @karthikraman
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python
software
tool
pythonsoftwaretool
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1The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism.
G. Birkel, A. Ghosh, V. Kumar, D. Weaver, D. Ando, T. Backman, A. Arkin, J. Keasling, and H. Mart\'ın. BMC bioinformatics, (Apr 5, 2017)
6 years ago by @karthikraman
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c13
flux-analysis
python
software
c13flux-analysispythonsoftware
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2GPU-powered model analysis with PySB/cupSODA.
L. Harris, M. Nobile, J. Pino, A. Lubbock, D. Besozzi, G. Mauri, P. Cazzaniga, and C. Lopez. Bioinformatics (Oxford, England), (Jun 28, 2017)
6 years ago by @karthikraman
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gpu
ode
python
software
gpuodepythonsoftware
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2Python data science handbook : essential tools for working with data
J. VanderPlas. O'Reilly Media, Inc, Sebastopol, CA, (2016)
7 years ago by @achakraborty
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2016
book
machine-learning
oreilly
python
software
2016bookmachine-learningoreillypythonsoftware
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2Python data science handbook : essential tools for working with data
J. VanderPlas. O'Reilly Media, Inc, Sebastopol, CA, (2016)
7 years ago by @marcsaric
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python
software
statistics
textbook
pythonsoftwarestatisticstextbook
(0)
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1Scikit-learn: Machine learning in Python
F. Pedregosa, G. Varoquaux, A. Gramfort, V. Michel, B. Thirion, O. Grisel, M. Blondel, P. Prettenhofer, R. Weiss, and V. Dubourg. Journal of Machine Learning Research, 12 (Oct): 2825--2830 (2011)
7 years ago by @lautenschlager
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lursurvey
machine-learning
python
software
lursurveymachine-learningpythonsoftware
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1COSMOS: Python library for massively parallel workflows
E. Gafni, L. Luquette, A. Lancaster, J. Hawkins, J. Jung, Y. Souilmi, D. Wall, and P. Tonellato. Bioinformatics, 30 (20): 2956-2958 (October 2014)
7 years ago by @marcsaric
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cloud-computing
fulltext
python
sequencing
software
workflow
cloud-computingfulltextpythonsequencingsoftwareworkflow
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1The Python Language Reference Manual
G. van Rossum, and F. Drake. Network Theory Ltd., (2011)
8 years ago by @salotz
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programming
programming-language
python
software
programmingprogramming-languagepythonsoftware
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2Scikit-learn: Machine learning in Python
F. Pedregosa, G. Varoquaux, A. Gramfort, V. Michel, B. Thirion, O. Grisel, M. Blondel, P. Prettenhofer, R. Weiss, V. Dubourg and 1 other author(s). Journal of Machine Learning Research, 12 (Oct): 2825--2830 (2011)
8 years ago by @salotz
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machine-learning
python
software
machine-learningpythonsoftware
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1mast: v0.2.0 release
salotz. (August 2016)
8 years ago by @salotz
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computational-biology
computational-chemistry
mastic
molecular-software
python
software
computational-biologycomputational-chemistrymasticmolecular-softwarepythonsoftware
(0)
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1HTMD: High-Throughput Molecular Dynamics for Molecular Discovery
S. Doerr, M. Harvey, F. Noé, and G. De Fabritiis. Journal of Chemical Theory and Computation, 12 (4): 1845-1852 (2016)PMID: 26949976.
8 years ago by @salotz
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molecular-dynamics
molecular-modelling
python
software
molecular-dynamicsmolecular-modellingpythonsoftware
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1HTSeq - a Python framework to work with high-throughput sequencing data.
S. Anders, P. Pyl, and W. Huber. Bioinformatics, 31 (2): 166-169 (January 2015)
8 years ago by @marcsaric
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EMBL
GDC
MUSTREAD
bioinformatics
fulltext
python
rna-seq
rpkm
sequencing
software
EMBLGDCMUSTREADbioinformaticsfulltextpythonrna-seqrpkmsequencingsoftware
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1Automatic Fitting of Binary Interaction Parameters for Multi-fluid Helmholtz-Energy-Explicit Mixture Models
I. Bell, and E. Lemmon. Journal of Chemical & Engineering Data, 61 (11): 3752-3760 (2016)
8 years ago by @thorade
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2016
Helmholtz
Python
binary
equation-of-state
fluid
mixture
multi-component
software
2016HelmholtzPythonbinaryequation-of-statefluidmixturemulti-componentsoftware
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1MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
R. McGibbon, K. Beauchamp, M. Harrigan, C. Klein, J. Swails, C. Hernández, C. Schwantes, L. Wang, T. Lane, and V. Pande. Biophysical Journal, 109 (8): 1528 - 1532 (2015)
8 years ago by @salotz
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molecular-dynamics
python
software
trajectory-analysis
molecular-dynamicspythonsoftwaretrajectory-analysis
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1EMMA: A Software Package for Markov Model Building and Analysis
M. Senne, B. Trendelkamp-Schroer, A. Mey, C. Schütte, and F. Noé. Journal of Chemical Theory and Computation, 8 (7): 2223-2238 (2012)PMID: 26588955.
8 years ago by @salotz
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markov-model-analysis
markov-state-models
python
software
markov-model-analysismarkov-state-modelspythonsoftware
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1PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
M. Scherer, B. Trendelkamp-Schroer, F. Paul, G. Pérez-Hernández, M. Hoffmann, N. Plattner, C. Wehmeyer, J. Prinz, and F. Noé. Journal of Chemical Theory and Computation, 11 (11): 5525-5542 (2015)PMID: 26574340.
8 years ago by @salotz
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markov-model-analysis
markov-state-models
python
software
markov-model-analysismarkov-state-modelspythonsoftware
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1PyPLIF: Python-based Protein-Ligand Interaction Fingerprinting
M. Radifar, N. Yuniarti, and E. Istyastono. Bioinformation, 9 (6): 325-328 (2013)
9 years ago by @salotz
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computational-biology
ligand-binding
ligand-docking
ligand-fingerprinting
noncovalent-interactions
python
software
computational-biologyligand-bindingligand-dockingligand-fingerprintingnoncovalent-interactionspythonsoftware
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