Scientific Computing and Data Management

bioSyntax: Syntax Highlighting For Computational Biology

bioSyntax provides syntax highlighting tools for computational biology data formats to improve readability and efficiency.

Container-based bioinformatics with Pachyderm

The paper demonstrates the use of Pachyderm for efficient and reproducible metabolomics workflows in bioinformatics.

Hot-starting software containers for bioinformatics analyses

The paper introduces a method to reduce cloud computing costs for bioinformatics by hot-starting software containers, avoiding repetitive initialization steps.

WAVES: a Web Application for Versatile Enhanced bioinformatic Services

WAVES provides a web application for integrating bioinformatic tools through web pages, forms, and a RESTful API, with support for running computations on Galaxy instances.

Kipoi: accelerating the community exchange and reuse of predictive models for genomics

Kipoi provides a framework for standardized, reusable machine learning models in genomics, enabling tasks like variant effect prediction and model benchmarking.

SATurn: A modular bioinformatics framework for the design of robust maintainable web-based and standalone applications

SATurn is a modular bioinformatics framework for creating maintainable web and standalone applications, used to build a bioinformatics portal supporting diverse scientific research.

Experimenting with reproducibility in bioinformatics

The paper attempts to reproduce a bioinformatics method, identifies challenges in reusability, and proposes solutions to improve reproducibility and research efficiency.

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis.

YAMP: a containerised workflow enabling reproducibility in metagenomics research

YAMP provides a containerised workflow for analysing whole shotgun metagenomic data, ensuring reproducibility and ease of use across UNIX-like systems.

Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse

Tellurium Notebook enables reproducible and reusable dynamical models in systems biology by integrating community standards and literate coding practices.

Lightweight bioinformatics: evaluating the utility of Single Board Computer (SBC) clusters for portable, scalable Real-Time Bioinformatics in fieldwork environments via benchmarking.

This study evaluates the use of Single Board Computers (SBCs) for portable, real-time bioinformatics in fieldwork by benchmarking their performance against laptops and cloud-based systems.

Practical computational reproducibility in the life sciences

The paper presents technologies that make computational reproducibility practical by integrating package management, containerization, and workflow systems.

SoS Notebook: An Interactive Multi-Language Data Analysis Environment

SoS Notebook provides a web-based environment for multi-language data analysis, enabling seamless integration of different scripting languages in bioinformatics workflows.

Porcupine: a visual pipeline tool for neuroimaging analysis

Porcupine is a visual tool that creates reproducible neuroimaging analysis pipelines by generating code and Docker environments, improving transparency and shareability.

Embedding containerized workflows inside data science notebooks enhances reproducibility

The paper introduces nbdocker, a Jupyter notebook extension that embeds Docker containers to enhance reproducibility of data science workflows.

Building online genomics applications using BioPyramid

BioPyramid provides a python package to streamline the development of online genomics applications with built-in tools for gene annotation, dataset management, and visualization.

Kafka interfaces for composable streaming genomics pipelines

The paper proposes using Kafka streams to improve genomic data processing pipelines by enabling scalable, fault-tolerant, and composable workflows.

TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses

BDQC: a general-purpose analytics tool for domain-blind validation of Big Data

BDQC identifies data outliers and anomalies in large-scale genomic pipelines without domain knowledge, improving data quality and enabling new insights.

Sequanix: A Dynamic Graphical Interface for Snakemake Workflows

Sequanix provides a graphical interface for Snakemake workflows to make them more accessible to a broader audience.

Visual Representation of Experimental Protocols

The paper introduces a new user interface for creating experimental protocols by manipulating diagrams to specify liquid handling operations.

Bioinformatics Workflow Management With The Wobidisco Ecosystem

The paper introduces a set of open-source workflow management tools for bioinformatics, emphasizing reliability and flexibility.

Biopipe: A Lightweight System Enabling Comparison of Bioinformatics Tools and Workflows

Biopipe simplifies bioinformatics workflow creation and execution, enabling tool comparison through a web interface and automated Docker-based setup.

Tribe: The collaborative platform for reproducible web-based analysis of gene sets

Tribe enables reproducible, collaborative gene set analysis across multiple bioinformatics webservers and tools.

Reproducible Bioconductor Workflows Using Browser-Based Interactive Notebooks And Containers

The paper introduces BiocImageBuilder, a tool that enables reproducible bioinformatics workflows through interactive notebooks and containers.

Enabling rapid cloud-based analysis of thousands of human genomes via Butler

Butler enables faster cloud-based analysis of thousands of human genomes by managing infrastructure, workflows, and execution with 43% increased throughput.

Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking

This paper describes OpenEBench, a continuous automated benchmarking system for bioinformatics methods, tools, and web services to improve reproducibility and interoperability.

Building Applications For Interactive Data Exploration In Systems Biology

The paper presents a microservice-based framework for building interactive data exploration tools in systems biology, demonstrating it with a breast cancer transcriptional analysis web application.

Automatic OpenAPI to Bio.tools Conversion

This paper introduces an interoperability layer to convert OpenAPI specifications to bio.tools annotations for FAIR web services.