Saravanan666/pypi-org huggingface dataset:
Package: biobb-guild
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-io
biobb_ioIntroductionBiobb_io is the Biobb module collection to fetch data to be consumed by the
rest of the Biobb building blocks.
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_io==4.1.0"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_io==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_io:4.1.0--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_io:4.1.0--pyhdfd78af_0 <command>The command list and specification can be found at theCommand Line documentation.Using SINGULARITY:MacOS users: it's strongly recommended to avoid Singularity and useDockeras containerization system.Installation:singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.1.0--pyhdfd78af_0Usage:singularity exec biobb_io.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-md
biobb_mdIntroductionBiobb_md is the Biobb module collection to perform 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.Versionv3.7.2 2021.3InstallationUsing 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_md>=3.7.2"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_md>=3.7.2"Usage: With conda installation BioBBs can be used with thePython API documentationand theCommand Line documentationUsing DOCKER:Installation:docker pull quay.io/biocontainers/biobb_md:3.7.2--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_md:3.7.2--pyhdfd78af_0 <command>Using SINGULARITY:MacOS users: it's strongly recommended to avoid Singularity and useDockeras containerization system.Installation:singularity pull --name biobb_md.sif shub://bioexcel/biobb_mdUsage:singularity exec biobb_md.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) 2015-2021Barcelona Supercomputing Center(c) 2015-2021Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-ml
biobb_mlIntroductionBiobb_ml is the Biobb module collection to perform machine learning predictions.
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_ml>=4.1.0"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_ml>=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_ml:4.1.0--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_ml: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_ml.sif https://depot.galaxyproject.org/singularity/biobb_ml:4.1.0--pyhdfd78af_0Usage:singularity exec biobb_ml.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-model
biobb_modelIntroductionBiobb_model is the Biobb module collection to check and model 3d structures,
create mutations or reconstruct missing atoms.
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 2023.4InstallationUsing 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_model>=4.1.0"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_model>=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_model:4.1.0--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_model: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_model.sif https://depot.galaxyproject.org/singularity/biobb_model:3.8.0--pyhdfd78af_0Usage:singularity exec biobb_model.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-pdb-tools
biobb_pdb_toolsIntroductionbiobb_pdb_tools is a swiss army knife for manipulating and editing PDB files.
The latest documentation of this package can be found in our readthedocs site:latest API documentation.Versionv4.1.1 2024.1InstallationUsing 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_pdb_tools>=4.1.1"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_pdb_tools>=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_pdb_tools:4.1.1--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_pdb_tools:4.1.1--pyhdfd78af_0 <command>Using SINGULARITY:MacOS users: it's strongly recommended to avoid Singularity and useDockeras containerization system.Installation:singularity pull --name biobb_pdb_tools.sif https://depot.galaxyproject.org/singularity/biobb_pdb_tools:4.1.1--pyhdfd78af_0Usage:singularity exec biobb_pdb_tools.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) 2015-2024Barcelona Supercomputing Center(c) 2015-2024Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-pmx
biobb_pmxIntroductionBiobb_pmx is the Biobb module collection to perform PMX (http://pmx.mpibpc.mpg.de) executions.
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 or DOCKER.Installation:pip install "biobb_pmx>=4.1.0"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_pmx>=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_pmx:4.1.0--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_pmx: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_pmx.sif https://depot.galaxyproject.org/singularity/biobb_pmx:4.1.0--pyhdfd78af_0Usage:singularity exec biobb_pmx.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) 2015-2022Barcelona Supercomputing Center(c) 2015-2022Institute for Research in BiomedicineLicensed under theApache License 2.0, see the file LICENSE for details.
Package: biobb-structure-checking
biobb_structure_checkingIntroductionBiobb_structure_checking provides a series of functions to check the quality of a 3D structure intended to facilitate the setup of a molecular dynamics simulation of protein or nucleic acids systems.Biobb_structure_checking package allows to configure the system (selection of model/chains,alternative location, addition of disulfide bonds and hydrogen atoms, side chain mutations), to detect and fix structure errors (missing side chain atoms, backbone breaks, amide assignments, incorrect chirality). It works with structures obtained from the Protein Data Bank or user provided.The Biobb_structure_checking package provides a command line utility (check_structure) and a pythonAPI.The latest documentation of this package can be found in our readthedocs site:latest package documentation.Versionv3.13.4 September 2024RequirementsBiopythonOptional requirementspsutil (required for --debug, included in conda pkg.)Modeller (required for some functionalities, not included in conda pkg.)jupyter & nglview (required for demonstration notebooks, not included in conda pkg.)InstallationUsing PIP:Important:PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA.Installation:pip install "biobb_structure_checking>=3.13.4"Usage:Python API documentation.Using ANACONDA:Installation:conda install -c bioconda "biobb_structure_checking>=3.13.4"Usage: With conda installation BioBBs can be used with thePython API documentationand theCommand Line documentationCopyright & LicensingThis software has been developed in the MMB group (http://mmb.irbbarcelona.org) at the
BSC (https://www.bsc.es/) & IRB (https://www.irbbarcelona.org/) for the European BioExcel (https://bioexcel.eu/), funded by the European Commission
(EU H2020675728).(c) 2015-2022Barcelona Supercomputing Center(c) 2015-2022Institute for Research in BiomedicineLicensed under theGNU Lesser General Public License v2.1.
Package: biobb-structure-utils
biobb_structure_utilsIntroductionBiobb_structure_utils is the Biobb module collection to modify or extract information from a PDB structure file, such as pulling out a particular model or chain, removing water molecules or ligands, or renumbering or sorting atoms or residues. 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_structure_utils>=4.1.0"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_structure_utils>=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_structure_utils:4.1.0--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_structure_utils: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_structure_utils.sif https://depot.galaxyproject.org/singularity/biobb_structure_utils:4.1.0--pyhdfd78af_0Usage:singularity exec biobb_structure_utils.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.AcknolegementsThis software uses functions to read and modify GRO files based in theGROPYlibrary created by Zhikun Cai (caizkun@gmail.com) under theMIT. In this projectGROPYhas been adapted to Python 3 and our own needs.
Package: biobb-vs
biobb_vsIntroductionBiobb_vs is the Biobb module collection to perform virtual screening studies.
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.At the time of publishing the current version,autodock_vina has not been compiled for the new ARM mac M1/M2 chips. So the vina.autodock_vina_run only work in these computers through docker containers.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 or DOCKER.Installation:pip install "biobb_vs>=4.1.1"Usage:Python API documentationUsing ANACONDA:Installation:conda install -c bioconda "biobb_vs>=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_vs:4.1.1--pyhdfd78af_0Usage:docker run quay.io/biocontainers/biobb_vs:4.1.1--pyhdfd78af_0 <command>Using SINGULARITY:MacOS users: it's strongly recommended to avoid Singularity and useDockeras containerization system.Installation:singularity pull --name biobb_vs.sif https://depot.galaxyproject.org/singularity/biobb_vs:4.1.1--pyhdfd78af_0Usage:singularity exec biobb_vs.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-wf-mutations
biobb_wf_mutationsIntroductionLysozyme + Mutations workflow built using BioBB Based on the official Gromacs tutorial:http://www.mdtutorials.com/gmx/lysozyme/01_pdb2gmx.htmlBiobb (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.VersionMarch 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: biobert-bern
Intro biobert-bernThis file will become your README and also the index of your
documentation.Installpipinstallbiobert_bernHow to useGrab functions from biobertApi notebook to use the BERN2 api that
automatically labels biomedical words located in the block of text that
you send itFound My Fitness ExampleHere we’ll try using elements from the biobertApi module to label
biomedical terms in the comments section of a Found My Fitness youtube
video that looks like this :>>
Package: biobert-embedding
BioBert EmbeddingsToken and sentence level embeddings from BioBERT model (Biomedical Domain).BERT, published by Google, is conceptually simple and empirically powerful as it obtained state-of-the-art results on eleven natural language processing tasks.The objective of this project is to obtain the word or sentence embeddings fromBioBERT, pre-trained model by DMIS-lab. BioBERT, which is a BERT language model further trained on PubMed articles for adapting biomedical domain.Instead of building and do fine-tuning for an end-to-end NLP model, You can directly utilize word embeddings from Biomedical BERT to build NLP models for various downstream tasks eg. Biomedical text classification, Text clustering, Extractive summarization or Entity extraction etc.FeaturesCreates an abstraction to remove dealing with inferencing pre-trained BioBERT model.Require only two lines of code to get sentence/token-level encoding for a text sentence.The package takes care of OOVs (out of vocabulary) inherently.Downloads and installs BioBERT pre-trained model (first initialization, usage in next section).Installpip install biobert-embedding==0.1.1Exampleword embeddings generated are list of 768 dimensional embeddings for each word.sentence embedding generated is 768 dimensional embedding which is average of each token.frombiobert_embedding.embeddingimportBiobertEmbeddingtext="Breast cancers with HER2 amplification have a higher risk of CNS metastasis and poorer prognosis."\# Class Initialization (You can set default 'model_path=None' as your finetuned BERT model path while Initialization)biobert=BiobertEmbedding()word_embeddings=biobert.word_vector(text)sentence_embedding=biobert.sentence_vector(text)print("Text Tokens: ",biobert.tokens)# Text Tokens:  ['breast', 'cancers', 'with', 'her2', 'amplification', 'have', 'a', 'higher', 'risk', 'of', 'cns', 'metastasis', 'and', 'poorer', 'prognosis', '.']print('Shape of Word Embeddings:%dx%d'%(len(word_embeddings),len(word_embeddings[0])))# Shape of Word Embeddings: 16 x 768print("Shape of Sentence Embedding = ",len(sentence_embedding))# Shape of Sentence Embedding =  768
Package: biobert-pytorch
BiobertologyReady to useBioBertpytorch weights forHuggingFacepytorchBertModel.To load the model:from biobertology import get_biobert, get_tokenizer

biobert = get_biobert(model_dir=None, download=True)
tokenizer = get_tokenizer()Example of fine tuning bioberthere.How was it converted to pytorch?Model weights have been downloaded fromhereand convertedby following the commands describedhere.pytorchSpecifically, using the command:pytorch_transformers bert biobert_v1.1_pubmed/model.ckpt-1000000 biobert_v1.1_pubmed/bert_config.json biobert_v1.1_pubmed/pytorch_model.binfollowed by the renaming of the config file:mv biobert_v1.1_pubmed/bert_config.json biobert_v1.1_pubmed/config.jsonall of the other files inside the original weights file have been deleted.