Saravanan666/pypi-org huggingface dataset:
Package: bio-attention
bio-attentionSimple implementations of attention modules adapted for the biological data domain.:construction: THIS CODE IS BEING ACTIVELY DEVELOPED :construction:Don't look for stability here (yet).Why use this package?There are already plenty of excellent implementations out there that allow you to test out the countless variants of transformers[1],[2].
This repository primarily separates itself from the previous in that it contains positional encodings schemes adapted to allow for irregularly-spaced positions in sequences.InstallSince PyTorch is a dependency ofbio-attention, we recommendinstalling PyTorchindependently first, as your system may require a specific version (e.g. CUDA drivers).After PyTorch installation,bio-attentioncan be installed usingpippipinstallbio-attentionNoteThis package used the be a 2D sliding window attention package. The current formulation of the package does not allow for this type of attention anymore (instead, I recommend to perform axial attention with alternating sliding window attention across one axis and full self-attention across the other). If you want to use 2D sliding window attention, check out theold version of this repo.UsagePackage roadmapEmbedding layersContinuousDiscreteBinaryBin[~] Positional encoding schemesSinusoidalEmbeddingContinuousRotaryAliBiDPBXLTest support for multi-dimensional inputs[~] Attention modulesVanillaWindowedRandomPerformerEncoderDecoderCrossSupport for multi-dim inputsAdd a warning if non-increasing positional indices are used with a decoder attentionAdd docs clarifying that clf tokens are automatically accounted for if no pos is provided for themTestsTypingDocs
Package: biobabel
Biobabel : a unified interface for reading a plethora of physiology file formatsMany different file formats exist for physiology signals such as cardiac (ECG, PPG) or respiratory data. Many packages exist in Python to read these formats but they load into different data structures. This package is a wrapper of sorts for already existing tools providing a unified easy-to-use interface.Installationpython3 -m pip install biobabelUsageCommand lineTo preview a file, use the provided script from the command line:biobabel <FILENAME>You can leave<FILENAME>blank in which case you will be prompted to select a file you want to preview.PythonSimple usage example in Python:import biobabel
bio = biobabel.load('filename.txt')
bio.print()
bio.plot()
bio.save('new_filename.hdf5')More complete overview of functionality inJupyter notebook.RequirementsPhysiology dialectsCurrently supported dialects are:EDF throughPyEDFliblabstreaminglayer (LSL) XDF (alpha) thanks topyxdfBioPAC Acknowledge (acq) thanks tobioreadopensignals ("OpenSignals (r)evolution" thanks toopensignalsreaderBiosemi BDF thanks topybdfGeneric CSV (where CSV delimiter is automatically inferred and the time column is guessed as well)Brams-Bio-Box (in-house format, even though the Generic-CSV functionality should take care of this now)hdphysio5 thanks tohdphysio5TeensyECG (in-house format)DevelopmentInstall latest development version from Github:python -m pip install "biobabel @ git+https://github.com/florisvanvugt/biobabel"Install locally:pip install .and editable:pip install -e .
Package: biobakery-workflows
bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters. Quality control and statistical summary reports are automatically generated for most data types, which include 16S amplicons, metagenomes, and metatranscriptomes. Workflows are run directly from the command line and tasks can be imported to create your own custom workflows. The workflows and tasks are built with AnADAMA2 which allows for parallel task execution locally and in a grid compute environment.
Package: biobank-tools
Biobank ToolsDocumentation:https://altaf-ali.github.io/biobank-toolsGitHub:https://github.com/altaf-ali/biobank-toolsPyPI:https://pypi.org/project/biobank-tools/FeaturesThe Biobank Tools package provides simple, fast, and efficient access to UK
Biobank data. Once you've downloaded and extracted the UK Biobank data to
comma or tab separated files, you can use Biobank Tools to convert the data
to a format that's better suited for searching and filtering than plain text
files. Internally, Biobank Tools convert the data toApache Parquetformat for optimized column-wise access.RequirementsBiobank Tools require Python 3.8 or above.CreditsThis package was created withCookiecutterand thealtaf-ali/cookiecutter-pypackageproject template.
Package: biobb
biobbIntroductionBiobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of our biobb collections can be found in our readthedocs sites:biobb_io[GitHub]: Biobb collection to fetch data to be consumed by the rest of the Biobbs.biobb_model[GitHub]: Biobb collection to check and model 3d protein structures.biobb_md[GitHub]: Biobb collection to perform molecular dynamics simulations.biobb_analysis[GitHub]: Biobb collection to perform analysis over molecular dynamics simulations.biobb_wf_mutations[GitHub]: Workflow performing molecular dynamics simulations of protein mutants.biobb_adapters[GitHub]: Biobb collection to use the building blocks with several workflow managers.biobb_common[GitHub]: Common tools to use the rest of the Biobb building blocks.biobb_template[GitHub]: Boilerplate code and template examples to create your own Biobbs.Versionv1.0.2 May 2019 ReleaseCopyright & LicensingThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the
BSC (http://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (http://bioexcel.eu/), funded by the European Commission
(EU H2020675728).(c) 2015-2019Barcelona Supercomputing Center(c) 2015-2019Institute for Research in BiomedicineLicensed under theApache License 2.0, see the fileLICENSEfor details.
Package: biobb-3dshaper
biobb_templateIntroductionBiobb_template is a complete code template to promote and facilitate the creation of
new Biobbs by the community.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv3.0.0 2021.3InstallationIf you have no experience with anaconda, please first take a look to theNew with anaconda?section of theofficial documentation.Download repositoryAlthough the biobb_template repository is available at GitHub and thus you can clone it, we strongly recommend you todownload it compressedand start your new project from scratch.Create new conda environmentOnce you have the project unzipped in your computer, please follow the next steps to create a new conda environment:cd biobb_template-masterconda env create -f conda_env/environment.ymlUpdate environment pathsEditconda_env/biobb_template.pthwith the paths to yourbiobb_templatefolder. Example:/home/user_name/projects/biobb_template//home/user_name/projects/biobb_template/biobb_template/biobb_templateCopy the editedconda_env/biobb_template.pthfile to the site-packages folder of your environment. This folder is in/[anaconda-path]/envs/biobb_template/lib/python3.7/site-packages, where/[anaconda-path]is usually/anaconda3or/opt/conda.cp conda_env/biobb_template.pth /[anaconda-path]/envs/biobb_template/lib/python3.7/site-packagesActivate environmentThen, activate the recently createdbiobb_templateconda environment:conda activate biobb_templateCreate repositoryThis template includes some folders not standard for a biobb, such asbiobb_template/adapters/,biobb_template/notebooks/orconda_env/. For the sake of having a pure biobb structure, you should uncomment the three last lines of the.gitignorefile before creating a new git repository:biobb_template/adaptersbiobb_template/notebooksconda_envThen, inialitize repository:git initBinary paths configurationAdditionally, it's recommendable to configure binary paths in your environment in order to ease the command line execution. More info about this subject in theBinary path configurationsection of theofficial documentation.DocumentationClick here to find the API Documentation examplefor this template andhere for Command Line documentation.And here you can findthe full documentationabout how to build a newBioExcel building blockfrom scratch.Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2020Barcelona Supercomputing Center(c) 2015-2020Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-adapters
biobb_adaptersIntroductionBiobb_adapters is the Biobb module collection to use the building blocks with several workflow managers.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Version4.0.0 2023.1Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2023Barcelona Supercomputing Center(c) 2015-2023Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-analysis
biobb_analysisIntroductionBiobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv4.1.0 2023.3InstallationUsing PIP:Important:PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY.Installation:pip install "biobb_analysis>=4.1.0"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_analysis>=4.1.0"Usage: With conda installation BioBBs can be used with thePython API documentationand theCommand Line documentationUsing DOCKER:Installation:docker pull quay.io/biocontainers/biobb_analysis:4.1.0--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_analysis:4.1.0--pyhdfd78af_0 <command>Using SINGULARITY:MacOS users: it's strongly recommended to avoid Singularity and useDockeras containerization system.Installation:singularity pull --name biobb_analysis.sif https://depot.galaxyproject.org/singularity/biobb_analysis:4.1.0--pyhdfd78af_0Usage:singularity exec biobb_analysis.sif <command>The command list and specification can be found at theCommand Line documentation.Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2023Barcelona Supercomputing Center(c) 2015-2023Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-chemistry
biobb_chemistryIntroductionBiobb_chemistry is the Biobb module collection to perform chemistry over molecular dynamics simulations.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv4.1.0 2023.3InstallationUsing PIP:Important:PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY.Installation:pip install "biobb_chemistry>=4.1.0"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_chemistry>=4.1.0"Usage: With conda installation BioBBs can be used with thePython API documentationand theCommand Line documentationUsing DOCKER:Installation:docker pull quay.io/biocontainers/biobb_chemistry:4.1.0--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_chemistry:4.1.0--pyhdfd78af_0 <command>Using SINGULARITY:MacOS users: it's strongly recommended to avoid Singularity and useDockeras containerization system.Installation:singularity pull --name biobb_chemistry.sif https://depot.galaxyproject.org/singularity/biobb_chemistry:4.1.0--pyhdfd78af_0Usage:singularity exec biobb_chemistry.sif <command>The command list and specification can be found at theCommand Line documentation.Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2023Barcelona Supercomputing Center(c) 2015-2023Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-cmip
biobb_cmipIntroductionBiobb_cmip is the Biobb module collection to compute classical molecular interaction potentials.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv4.1.0 2023.3InstallationUsing PIP:Important:PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY.Installation:pip install "biobb_cmip>=4.1.0"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_cmip>=4.1.0"Usage: With conda installation BioBBs can be used with thePython API documentationand theCommand Line documentationUsing DOCKER:Installation:docker pull quay.io/biocontainers/biobb_cmip:4.1.0--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_cmip:4.1.0--pyhdfd78af_0 <command>Using SINGULARITY:MacOS users: it's strongly recommended to avoid Singularity and useDockeras containerization system.Installation:singularity pull --name biobb_cmip.sif https://depot.galaxyproject.org/singularity/biobb_cmip:4.1.0--pyhdfd78af_0Usage:singularity exec biobb_cmip.sif <command>The command list and specification can be found at theCommand Line documentation.Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2023Barcelona Supercomputing Center(c) 2015-2023Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-common
biobb_commonIntroductionBiobb_common is the base package required to use the biobb
packages.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv4.1.0 2023.1Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2023Barcelona Supercomputing Center(c) 2015-2023Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-disc4alldata
biobb_disgenetIntroductionBiobb_template is a complete code template to promote and facilitate the creation of
new Biobbs by the community.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv3.0.0 2021.3InstallationIf you have no experience with anaconda, please first take a look to theNew with anaconda?section of theofficial documentation.Download repositoryAlthough the biobb_template repository is available at GitHub and thus you can clone it, we strongly recommend you to [download it compressed]and start your new project from scratch.Activate the envSince the Bioconda package is not ready, after the download of the directory is necessary to set up the conda environment for the right functioning:conda create conda_env/environment.yml
conda activate biobb_disgenetIf the package is not working, set it up manually:python setup.py build
python setup.py installBinary paths configurationAdditionally, it's recommendable to configure binary paths in your environment in order to ease the command line execution. More info about this subject in theBinary path configurationsection of theofficial documentation.DocumentationClick here to find the API Documentation examplefor this template andhere for Command Line documentation.And here you can findthe full documentationabout how to build a newBioExcel building blockfrom scratch.Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2020Barcelona Supercomputing Center(c) 2015-2020Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-disgenet
biobb_disgenetIntroductionBiobb_template is a complete code template to promote and facilitate the creation of
new Biobbs by the community.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv3.0.0 2021.3InstallationIf you have no experience with anaconda, please first take a look to theNew with anaconda?section of theofficial documentation.Download repositoryAlthough the biobb_template repository is available at GitHub and thus you can clone it, we strongly recommend you to [download it compressed]and start your new project from scratch.Activate the envSince the Bioconda package is not ready, after the download of the directory is necessary to set up the conda environment for the right functioning:conda create conda_env/environment.yml
conda activate biobb_disgenetIf the package is not working, set it up manually:python setup.py build
python setup.py installBinary paths configurationAdditionally, it's recommendable to configure binary paths in your environment in order to ease the command line execution. More info about this subject in theBinary path configurationsection of theofficial documentation.DocumentationClick here to find the API Documentation examplefor this template andhere for Command Line documentation.And here you can findthe full documentationabout how to build a newBioExcel building blockfrom scratch.Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2020Barcelona Supercomputing Center(c) 2015-2020Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-dna
biobb_dnaIntroductionBiobb_dna is a package composed of different analyses for
nucleic acid trajectories and helical parameters.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv4.1.0 2023.3InstallationUsing PIP:Important:PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY.Installation:pip install "biobb_dna>=4.1.0"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_dna>=4.1.0"Usage: With conda installation BioBBs can be used with thePython API documentationand theCommand Line documentationUsing DOCKER:Installation:docker pull quay.io/biocontainers/biobb_dna:4.1.0--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_dna:4.1.0--pyhdfd78af_0 <command>Using SINGULARITY:MacOS users: it's strongly recommended to avoid Singularity and useDockeras containerization system.Installation:singularity pull --name biobb_dna.sif https://depot.galaxyproject.org/singularity/biobb_dna:4.1.0--pyhdfd78af_0Usage:singularity exec biobb_dna.sif <command>The command list and specification can be found at theCommand Line documentation.Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2023Barcelona Supercomputing Center(c) 2015-2023Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-gromacs
biobb_gromacsIntroductionbiobb_gromacs is the Biobb module collection to perform molecular dynamics simulations using the GROMACS MD suite.
Biobb (BioExcel building blocks) packages are Python building blocks that
create new layer of compatibility and interoperability over popular
bioinformatics tools.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv4.1.1 2023.3InstallationUsing PIP:Important:PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY.Installation:pip install "biobb_gromacs>=4.1.1"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_gromacs>=4.1.1"Usage: With conda installation BioBBs can be used with thePython API documentationand theCommand Line documentationUsing DOCKER:Installation:docker pull quay.io/biocontainers/biobb_gromacs:4.1.1--pyhdfd78af_1Usage:docker run quay.io/biocontainers/biobb_gromacs:4.1.1--pyhdfd78af_1 <command>Using SINGULARITY:MacOS users: it's strongly recommended to avoid Singularity and useDockeras containerization system.Installation:singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:4.1.1--pyhdfd78af_1Usage:singularity exec biobb_gromacs.sif <command>The command list and specification can be found at theCommand Line documentation.Copyright & LicensingThis software has been developed in theMMB groupat theBSC&IRBfor theEuropean BioExcel, funded by the European Commission (EU H2020823830, EU H2020675728).(c) 2015-2023Barcelona Supercomputing Center(c) 2015-2023Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.