Scientific Computing and Data Management

The paper introduces a reproducible bioinformatics project framework using Docker and R to ensure consistent and replicable analysis workflows across different systems.

HPCI is a Perl module that allows bioinformatics pipelines to run on different cluster types by abstracting cluster-specific APIs.

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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