Related papers: DataDeps.jl: Repeatable Data Setup for Replicable …
Motivation: Peptides have attracted the attention in this century due to their remarkable therapeutic properties. Computational tools are being developed to take advantage of existing information, encapsulating knowledge and making it…
Reproducibility in research remains hindered by complex systems involving data, models, tools, and algorithms. Studies highlight a reproducibility crisis due to a lack of standardized reporting, code and data sharing, and rigorous…
Large language models (LLMs) have shown impressive performance on general-purpose tasks, yet adapting them to specific domains remains challenging due to the scarcity of high-quality domain data. Existing data synthesis tools often struggle…
As software has become an integral part of scientific workflows, reproducible research practices must take it into account. In what way? Archiving source code is a necessary but insufficient condition. The ability to redeploy software…
The increasingly collaborative, globalized nature of scientific research combined with the need to share data and the explosion in data volumes present an urgent need for a scientific data management system (SDMS). An SDMS presents a…
The best way to calculate statistics from medical data is to use the data of individual patients. In some settings, this data is difficult to obtain due to privacy restrictions. In Germany, for example, it is not possible to pool routine…
GomalizingFlow.jl: is a package to generate configurations for quantum field theory on the lattice using the flow based sampling algorithm in Julia programming language. This software serves two main purposes: to accelerate research of…
We introduce DiffOpt.jl, a Julia library to differentiate through the solution of optimization problems with respect to arbitrary parameters present in the objective and/or constraints. The library builds upon MathOptInterface, thus…
MacroEnergy.jl (aka Macro) is an open-source framework for multi-sector capacity expansion modeling and analysis of macro-energy systems. It is written in Julia and uses the JuMP package to interface with a wide range of mathematical…
Science depends heavily on reliable and easy-to-use software packages, such as mathematical libraries or data analysis tools. Developing such packages requires a lot of effort, which is too often avoided due to the lack of funding or…
Like many groups considering the new programming language Julia, we faced the challenge of accessing the algorithms that we develop in Julia from R. Therefore, we developed the R package JuliaConnectoR, available from the CRAN repository…
Stimela2 is a new-generation framework for developing data reduction workflows. It is designed for radio astronomy data but can be adapted for other data processing applications. Stimela2 aims at the middle ground between ease of…
Spreadsheets provide a flexible and easy to use software development environment, but that leads to error proneness. Work has been done to prevent errors in spreadsheets, including using models to specify distinct parts of a spreadsheet as…
Recursive query processing has experienced a recent resurgence, as a result of its use in many modern application domains, including data integration, graph analytics, security, program analysis, networking and decision making. Due to the…
While the Machine Learning (ML) landscape is evolving rapidly, there has been a relative lag in the development of the "learning systems" needed to enable broad adoption. Furthermore, few such systems are designed to support the specialized…
Data models are necessary for the birth of data and of any data-driven system. Indeed, every algorithm, every machine learning model, every statistical model, and every database has an underlying data model without which the system would…
Java implementations of algorithms used by spreadsheets to automatically recompute the set of cells dependent on a changed cell are described using a mathematical model for spreadsheets based on graph theory. These solutions comprise part…
The D4M tool was developed to address many of today's data needs. This tool is used by hundreds of researchers to perform complex analytics on unstructured data. Over the past few years, the D4M toolbox has evolved to support connectivity…
In today's Web and social network environments, query workloads include ad hoc and OLAP queries, as well as iterative algorithms that analyze data relationships (e.g., link analysis, clustering, learning). Modern DBMSs support ad hoc and…
Whole Tale http://wholetale.org is a web-based, open-source platform for reproducible research supporting the creation, sharing, execution, and verification of "Tales" for the scientific research community. Tales are executable research…