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kallisto

kallisto: A command-line interface to simplify computational modelling and the generation of atomic features - Published in JOSS (2021)

https://github.com/astrazeneca/kallisto

Science Score: 93.0%

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    Found 7 DOI reference(s) in README and JOSS metadata
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    Published in Journal of Open Source Software

Keywords

chemistry computational-chemistry machinelearning quantum-chemistry

Keywords from Contributors

mesh

Scientific Fields

Mathematics Computer Science - 84% confidence
Last synced: 6 months ago · JSON representation

Repository

Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.

Basic Info
Statistics
  • Stars: 65
  • Watchers: 3
  • Forks: 20
  • Open Issues: 4
  • Releases: 9
Topics
chemistry computational-chemistry machinelearning quantum-chemistry
Created about 5 years ago · Last pushed about 2 years ago
Metadata Files
Readme Contributing License Code of conduct

README.md

Kallisto

PyPI - Python Version Documentation Maturity Level Tests codecov status

Table of Contents

  • Full Author List
  • Introduction
  • Installation
  • Testing suite
  • Reference

Full Author List

Introduction

We developed the kallisto program for the efficient and robust calculation of atomic features using molecular geometries either in a xmol or a Turbomole format. Furthermore, several modelling tools are implemented, e.g., to calculate root-mean squared deviations via quaternions (including rotation matrices), sorting of molecular geometries and many more. All features of kallisto are described in detail within our documentation (GitBook repository).

Main dependencies

bash click 7.1.2 Composable command line interface toolkit numpy 1.20.1 NumPy is the fundamental package for array computing with Python. scipy 1.6.0 SciPy: Scientific Library for Python └── numpy >=1.16.5

For a list of all dependencies have a look at the pyproject.toml file.

Installation from PyPI

To install kallisto via pip use our published PyPI package

bash pip install kallisto

Installation from Source

Requirements to install kallistofrom sources:

First check that poetry is running correctly (v1.0.10 at the time of writing)

```bash

poetry --version Poetry version 1.0.10 ```

Create a virtual environment (via pyenv or conda) and activate it. Afterwards, clone the kallisto project from GitHub and install it using poetry

```bash

git clone git@github.com:AstraZeneca/kallisto.git cd kallisto poetry install ```

Testing suite

The kallisto project uses nox as an automated unit test suite, which is therefore an additional dependency.

Default nox session

The default session includes: linting (lint), type checks (mypy, pytype), and unit tests (tests).

```bash

nox ```

When everything runs smoothly through, you are ready to go! After one successful nox run, we can reuse the created virtual environment via the -r flag.

```bash

nox -r ```

Different unit test sessions are implemented (check the noxfile.py). They can be called separately via the run session -rs flag.

Tests

Run all unit tests that are defined in the /tests directory.

```bash

nox -rs tests ```

Lint

kallisto uses the flake8 linter (check the .flake8 config file).

```bash

nox -rs lint ```

Black

kallisto uses the black code formatter.

```bash

nox -rs black ```

Safety

kallisto checks the security of dependencies via safety.

```bash

nox -rs safety ```

Mypy

kallisto checks for static types via mypy (check the mypy.ini config file).

```bash

nox -rs mypy ```

Pytype

kallisto furthermore uses pytype for type checks.

```bash

nox -rs pytype ```

Coverage

Unit test coverage can be checked as well.

```bash

nox -rs coverage ```

Reference

Always cite:

Eike Caldeweyher, J. Open Source Softw., 2021, 6, 3050. DOI: 10.21105/joss.03050

@article{Caldeweyher2021, doi = {10.21105/joss.03050}, url = {https://doi.org/10.21105/joss.03050}, year = {2021}, volume = {6}, number = {60}, pages = {3050}, author = {Eike Caldeweyher}, title = {kallisto: A command-line interface to simplify computational modelling and the generation of atomic features}, journal = {J. Open Source Softw.} }

Owner

  • Name: AstraZeneca
  • Login: AstraZeneca
  • Kind: organization
  • Location: Global

Data and AI: Unlocking new science insights

JOSS Publication

kallisto: A command-line interface to simplify computational modelling and the generation of atomic features
Published
April 15, 2021
DOI
Volume 6, Issue 60, Page 3050
Authors
Eike Caldeweyher ORCID
Data Science and Modelling, Pharmaceutical Science, R&D, AstraZeneca, Gothenburg, Sweden
Editor
Richard Gowers ORCID
Tags
Poetry Atomic Features Machine Learning Computational Chemistry Pharmaceutical Science
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FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs
Last synced: 4 months ago
Notch signaling drives development of Barrett’s metaplasia from Dclk1-positive epithelial tuft cells in the murine gastric mucosa
Last synced: 4 months ago
Changes in the gene expression profile during spontaneous migraine attacks
Last synced: 4 months ago
RNA-Seq identifies genes whose proteins are transformative in the differentiation of cytotrophoblast to syncytiotrophoblast, in human primary villous and BeWo trophoblasts
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Environment-dependent striatal gene expression in the BACHD rat model for Huntington disease
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Phylogenetic analyses and in-seedling expression of ammonium and nitrate transporters in wheat
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Physiological characterization of the emergence from diapause: A transcriptomics approach
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IRF-1 expressed in the inner cell mass of the porcine early blastocyst enhances the pluripotency of induced pluripotent stem cells
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Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses
Last synced: 4 months ago
Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System
Last synced: 4 months ago
Metagenomic Quantification of Genes with Internal Standards
Last synced: 4 months ago
An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin
Last synced: 4 months ago
Salmonella enterica Serovar Typhimurium SPI-1 and SPI-2 Shape the Global Transcriptional Landscape in a Human Intestinal Organoid Model System
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Functional and Comparative Analysis of Centromeres Reveals Clade-Specific Genome Rearrangements in <i>Candida auris</i> and a Chromosome Number Change in Related Species
Last synced: 4 months ago
The Candida albicans TOR-Activating GTPases Gtr1 and Rhb1 Coregulate Starvation Responses and Biofilm Formation
Last synced: 4 months ago
<i>Neisseria gonorrhoeae</i> Exposed to Sublethal Levels of Hydrogen Peroxide Mounts a Complex Transcriptional Response
Last synced: 4 months ago
Genomewide Analysis of Mode of Action of the <i>S</i> -Adenosylmethionine Analogue Sinefungin in Leishmania infantum
Last synced: 4 months ago
Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum
Last synced: 4 months ago
Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
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Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification
Last synced: 4 months ago
Germinal center–dependent and –independent memory B cells produced throughout the immune response
Last synced: 4 months ago
Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi
Last synced: 4 months ago
Practical guide for managing large-scale human genome data in research
Last synced: 4 months ago
Single‐Cell RNA Sequencing for Precision Oncology: Current State-of-Art
Last synced: 4 months ago
DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors
Last synced: 4 months ago
Niche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic Pathways
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Transient intracellular acidification regulates the core transcriptional heat shock response
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Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19
Last synced: 4 months ago
GTPBP1 resolves paused ribosomes to maintain neuronal homeostasis
Last synced: 4 months ago
Intergenerational epigenetic inheritance of cancer susceptibility in mammals
Last synced: 4 months ago
MEIS-mediated suppression of human prostate cancer growth and metastasis through HOXB13-dependent regulation of proteoglycans
Last synced: 4 months ago
Distinct mitochondrial defects trigger the integrated stress response depending on the metabolic state of the cell
Last synced: 4 months ago
Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium
Last synced: 4 months ago
Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Last synced: 4 months ago
Defects in translation-dependent quality control pathways lead to convergent molecular and neurodevelopmental pathology
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A genetic, genomic, and computational resource for exploring neural circuit function
Last synced: 4 months ago
Genetics of trans-regulatory variation in gene expression
Last synced: 4 months ago
Immune genes are hotspots of shared positive selection across birds and mammals
Last synced: 4 months ago
NHR-8 and P-glycoproteins uncouple xenobiotic resistance from longevity in chemosensory C. elegans mutants
Last synced: 4 months ago
Tissue-autonomous immune response regulates stress signaling during hypertrophy
Last synced: 4 months ago
Specificity of the Metallothionein-1 Response by Cadmium-Exposed Normal Human Urothelial Cells
Last synced: 4 months ago
Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation
Last synced: 4 months ago
A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress
Last synced: 4 months ago
Gastric Corpus Mucosal Hyperplasia and Neuroendocrine Cell Hyperplasia, but not Spasmolytic Polypeptide-Expressing Metaplasia, Is Prevented by a Gastrin Receptor Antagonist in H+/K+ATPase Beta Subunit Knockout Mice
Last synced: 4 months ago
Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana
Last synced: 4 months ago
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.
Last synced: 4 months ago
Distinct Regulation of the Expression of Satellite DNAs in the Beetle Tribolium castaneum
Last synced: 4 months ago
Priming with a Seaweed Extract Strongly Improves Drought Tolerance in Arabidopsis
Last synced: 4 months ago
Transcriptome Analysis of Seed Weight Plasticity in Brassica napus
Last synced: 4 months ago
A Gene Expression Signature to Predict Nucleotide Excision Repair Defects and Novel Therapeutic Approaches
Last synced: 4 months ago
A Transcriptome-Wide Isoform Landscape of Melanocytic Nevi and Primary Melanomas Identifies Gene Isoforms Associated with Malignancy
Last synced: 4 months ago
Detecting and Profiling Endogenous RNA G-Quadruplexes in the Human Transcriptome
Last synced: 4 months ago
Improving oligo-conjugated antibody signal in multimodal single-cell analysis
Last synced: 4 months ago
HLA class I loss in metachronous metastases prevents continuous T cell recognition of mutated neoantigens in a human melanoma model
Last synced: 4 months ago
Global isoform-specific transcript alterations and deregulated networks in clear cell renal cell carcinoma
Last synced: 4 months ago
Genomic and neoantigen evolution from primary tumor to first metastases in head and neck squamous cell carcinoma
Last synced: 4 months ago
TPM, FPKM, or Normalized Counts? A Comparative Study of Quantification Measures for the Analysis of RNA-seq Data from the NCI Patient-Derived Models Repository
Last synced: 4 months ago
Targeting Methylglyoxal in Diabetic Kidney Disease Using the Mitochondria-Targeted Compound MitoGamide
Last synced: 4 months ago
Transcriptomic analysis at organ and time scale reveals gene regulatory networks controlling the sulfate starvation response of Solanum lycopersicum
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Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
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Role of Transportome in the Gills of Chinese Mitten Crabs in Response to Salinity Change: A Meta-Analysis of RNA-Seq Datasets
Last synced: 4 months ago
Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines
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Alternative promoters control UGT2B17-dependent androgen catabolism in prostate cancer and its influence on progression
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Evaluation of the upregulation and surface expression of hypoxanthine guanine phosphoribosyltransferase in acute lymphoblastic leukemia and Burkitt’s B cell lymphoma
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A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
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The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells
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Assessment of the ptxD gene as a growth and selective marker in Trichoderma atroviride using Pccg6, a novel constitutive promoter
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Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility
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Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia
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Single-cell RNA-sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium
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DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories
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Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis
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Characterization of the β-tubulin gene family in Ascaris lumbricoides and Ascaris suum and its implication for the molecular detection of benzimidazole resistance
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CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells
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Transcriptome analysis indicates dominant effects on ribosome and mitochondrial function of a premature termination codon mutation in the zebrafish gene psen2
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Single cell RNA sequencing reveals regional heterogeneity of hepatobiliary innate lymphoid cells in a tissue-enriched fashion
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Two-step mixed model approach to analyzing differential alternative RNA splicing
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Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq
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A systematic performance evaluation of clustering methods for single-cell RNA-seq data
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DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
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Fast analysis of scATAC-seq data using a predefined set of genomic regions
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Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
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Pseudohyphal differentiation in Komagataella phaffii: investigating the FLO gene family
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Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data
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Comprehensive Analysis of mRNA and lncRNA Transcriptomes Reveals the Differentially Hypoxic Response of Preadipocytes During Adipogenesis
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Astrovirus replication in human intestinal enteroids reveals multi-cellular tropism and an intricate host innate immune landscape
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Host-derived circular RNAs display proviral activities in Hepatitis C virus-infected cells
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EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape
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Of eyes and embryos: subfunctionalization of the<i>CRX</i>homeobox gene in mammalian evolution
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Slaying the last unicorn: discovery of histones in the microalga <i>Nanochlorum eucaryotum</i>
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Differential gene expression indicates modulated responses to chronic and intermittent hypoxia in corallivorous fireworms (Hermodice carunculata)
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FADU: a Quantification Tool for Prokaryotic Transcriptomic Analyses
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Molecular and Physiological Adaptations to Low Temperature in <i>Thioalkalivibrio</i> Strains Isolated from Soda Lakes with Different Temperature Regimes
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Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing
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XCL1 expression correlates with CD8-positive T cells infiltration and PD-L1 expression in squamous cell carcinoma arising from mature cystic teratoma of the ovary
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Beta-catenin signaling regulates barrier-specific gene expression in circumventricular organ and ocular vasculatures
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FMRP promotes RNA localization to neuronal projections through interactions between its RGG domain and G-quadruplex RNA sequences
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16p11.2 microdeletion imparts transcriptional alterations in human iPSC-derived models of early neural development
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Gain-of-function mutations in the UNC-2/CaV2α channel lead to excitation-dominant synaptic transmission in Caenorhabditis elegans
Last synced: 4 months ago
Hippocampal transcriptome analysis following maternal separation implicates altered RNA processing in a mouse model of fetal alcohol spectrum disorder
Last synced: 4 months ago
Protein velocity and acceleration from single-cell multiomics experiments
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GitHub Events

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Last Year
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Committer Domains (Top 20 + Academic)
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Packages

  • Total packages: 13
  • Total downloads:
    • pypi 845 last-month
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 5
    (may contain duplicates)
  • Total versions: 28
  • Total maintainers: 2
pypi.org: kallisto

The Kallisto software enables the efficient calculation of atomic features that can be used within a quantitative structure-activity relationship (QSAR) approach. Furthermore, several modelling helpers are implemented.

  • Versions: 9
  • Dependent Packages: 2
  • Dependent Repositories: 5
  • Downloads: 845 Last month
Rankings
Dependent packages count: 2.1%
Dependent repos count: 6.7%
Average: 7.2%
Forks count: 8.4%
Stargazers count: 9.2%
Downloads: 9.4%
Maintainers (1)
ehjc
Last synced: 6 months ago
alpine-v3.18: py3-kallisto

Efficiently calculate 3D-atomic/molecular features for quantitative structure-activity relationship approaches

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 11.1%
Forks count: 21.8%
Stargazers count: 22.5%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.18: py3-kallisto-pyc

Precompiled Python bytecode for py3-kallisto

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 11.1%
Forks count: 21.8%
Stargazers count: 22.5%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-edge: py3-kallisto

Efficiently calculate 3D-atomic/molecular features for quantitative structure-activity relationship approaches

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 14.6%
Average: 15.3%
Forks count: 22.7%
Stargazers count: 23.9%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-edge: py3-kallisto-pyc

Precompiled Python bytecode for py3-kallisto

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 14.3%
Average: 15.6%
Forks count: 23.5%
Stargazers count: 24.6%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.21: py3-kallisto-pyc

Precompiled Python bytecode for py3-kallisto

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.22: py3-kallisto

Efficiently calculate 3D-atomic/molecular features for quantitative structure-activity relationship approaches

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.21: py3-kallisto

Efficiently calculate 3D-atomic/molecular features for quantitative structure-activity relationship approaches

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.19: py3-kallisto

Efficiently calculate 3D-atomic/molecular features for quantitative structure-activity relationship approaches

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.22: py3-kallisto-pyc

Precompiled Python bytecode for py3-kallisto

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.20: py3-kallisto-pyc

Precompiled Python bytecode for py3-kallisto

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.19: py3-kallisto-pyc

Precompiled Python bytecode for py3-kallisto

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago
alpine-v3.20: py3-kallisto

Efficiently calculate 3D-atomic/molecular features for quantitative structure-activity relationship approaches

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 100%
Maintainers (1)
iztok@iztok-jr-fister.eu
Last synced: 6 months ago

Dependencies

pyproject.toml pypi
  • black ^19.10b0 develop
  • codecov ^2.1.8 develop
  • coverage ^5.2 develop
  • flake8 ^3.8.3 develop
  • flake8-bandit ^2.1.2 develop
  • flake8-black ^0.2.0 develop
  • flake8-bugbear ^20.1.4 develop
  • flake8-import-order ^0.18.1 develop
  • mypy ^0.782 develop
  • pytest ^5.2 develop
  • pytest-cov ^2.10.0 develop
  • pytype ^2020.6.26 develop
  • safety ^1.9.0 develop
  • click ^7.1.2
  • numpy ^1.19.0
  • python ^3.7
  • scipy ^1.5.2
.github/workflows/black.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
.github/workflows/codeql.yml actions
  • actions/checkout v2 composite
  • github/codeql-action/analyze v1 composite
  • github/codeql-action/autobuild v1 composite
  • github/codeql-action/init v1 composite
.github/workflows/coverage.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite
.github/workflows/draft-pdf.yml actions
  • actions/checkout v2 composite
  • actions/upload-artifact v1 composite
  • openjournals/openjournals-draft-action master composite
.github/workflows/tests.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v1 composite