20 papers · ranked by Valyu relevance
Daniel Ortiz-Martínez
Background Bioinformatics data analysis faces significant challenges. As data analysis often takes the form of pipelines or workflows, workflow managers (WfMs) have become essential. Data flow programming constitutes the preferred approach in WfMs, enabling parallel processes activated reactively based on input…
Andy Vidan, Lars Fiedler
— This paper introduces a computing framework that combines Flow-Based Programming (FBP) and Large Language Models (LLMs) to enable Just-In-Time Programming (JITP). JITP empowers users, regardless of their programming expertise, to actively participate in the development and automation process by leveraging their…
Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
The complex nature of biological data has driven the development of specialized software tools. Scientific workflow management systems simplify the assembly of such tools into pipelines and assist with job automation and aids reproducibility of analyses. Many contemporary workflow tools are specialized and not designed…
Wilhelm Hasselbring, Maik Wojcieszak, Schahram Dustdar
When we consider the application layer [1] of networked infrastructures, data and control flow are important concerns in distributed systems integration. Modularity is a fundamental principle in software design [2], in particular for distributed system architectures. Modularity emphasizes high cohesion of individual…
Samuel Lampa, Martin Dahlö, Jonathan Alvarsson, Ola Spjuth
The Go programming language (referred to hereafter as ”Go”) was developed by Robert Griesemer, Rob Pike, and Ken Thompson at Google to provide a statically typed and compiled language that makes it easier to build highly concurrent programs that can also make good use of multiple CPU cores (i.e., “parallel program”) in…
Authors not listed
Self-driving laboratories (SDLs) promise accelerated scientific discovery and product development by closing the loop between robotic execution and AI/ML-driven decision making. In practice, however, SDL orchestration remains fragmented; workflows are typically encoded as laboratory-specific scripts or bespoke…
Baltasar Trancón y Widemann, Markus Lepper
The field of declarative stream programming (discrete time, clocked synchronous, modular, datacentric) is divided between the data-flow graph paradigm favored by domain experts, and the functional reactive paradigm favored by academics. In this paper, we describe the foundations of a framework for unifying functional…
Moslem Amiri, Fahad Manzoor Siddiqui, Colm Kelly, Roger Woods + 2 more
'Karen Rafferty' 'Burak Bardak'] With security and surveillance, there is an increasing need to process image data efficiently and effectively either at source or in a large data network. Whilst a Field-Programmable Gate Array has been seen as a key technology for enabling this, the design process has been viewed as…
Menachem Sklarz, Michal Gordon, Vered Chalifa-Caspi
Bioinformatics workflows (WFs) in general, and those involving High Throughput Sequencing data in particular, typically involve executing a sequence of programs on raw sequence files from as many as thousands of samples. Management of these WFs is laborious and error-prone. We have developed NeatSeq-Flow, a python…
Jiacheng Liu, Yuanchun Li, Liangyan Li, Yi Sun + 4 more
'Xiangyu Li' 'Yao Guo' 'Yunxin Liu'] Jiacheng Liu1,2,, Yuanchun Li1,5,, Liangyan Li3 , Yi Sun1 , Hao Wen1 , Xiangyu Li1 , Yao Guo4 and Yunxin Liu1,5 1 Institute of AI Industry Research (AIR), Tsinghua University, 2Beijing Institute of Technology, 3University of Science and Technology Beijing, 4Peking University…
Fernando H. C. Dias, Lucia Williams, Brendan Mumey, Alexandru I. Tomescu
Minimum flow decomposition (MFD) - the problem of finding a minimum set of weighted source-to-sink paths that perfectly decomposes a flow - is a classical problem in Computer Science, and variants of it are powerful models in a different fields such as Bioinformatics and Transportation. Even on acyclic graphs, the…
Michael A. Bukatin, Steve Matthews
We consider two classes of stream-based computations which admit taking linear combinations of execution runs: probabilistic sampling and generalized animation. The dataflow architecture is a natural platform for programming with streams. The presence of linear combinations allows us to introduce the notion of almost…
Rui Lu, Zhichuan Guo, José de Jesús Rangel Magdaleno
Compared to a stateless data plane, a stateful data plane offloads part of state information and control logic from a controller to a data plane to reduce communication overhead and improve packet processing efficiency. However, existing methods for implementing stateful data planes face challenges, particularly…
Jason P. Kurs, Manuele Simi, Fabien Campagne
Computational workflows and pipelines are often created to automate series of processing steps. For instance, workflows enable one to standardize analysis for large projects or core facilities, but are also useful for individual biologists who need to perform repetitive data processing. Some workflow systems, designed…
Shixiang Wang
Bioinformatics analyses depend on workflow engines to coordinate dozens of computational tools across complex dependency chains. The most widely adopted engines—Snakemake, Nextflow, the Common Workflow Language (CWL), and the Workflow Description Language (WDL)—run on interpreted or just-in-time (JIT) compiled language…
Cheng Wang, Hee Yong Youn
The usage of multiple flow tables (MFT) has significantly extended the flexibility and applicability of software-defined networking (SDN). However, the size of MFT is usually limited due to the use of expensive ternary content addressable memory (TCAM). Moreover, the pipeline mechanism of MFT causes long flow…
Lakshani Weerarathna, Oliver Weismantel, Tanja Junkers
A fully automated robotic synthesizer for the screening of amphiphilic block copolymer nanoparticle synthesis is presented. To reach this aim, block copolymer solutions are mixed in continuous flow with water, allowing for the automated variation of overall polymer concentration, mixing ratio of the water and organic…
Peter Sagmeister, Lukas Melnizky, Jason Williams, C. Oliver Kappe
In modern pharmaceutical research, the demand for expeditious development of synthetic routes to active pharmaceutical ingredients (APIs) has led to a paradigm shift towards data-rich process development. Conventional methodologies en-compass prolonged timelines for reaction and analytical model developments. Both…
Mark P Waller, Thomas Dresselhaus, Jack Yang
Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code.…
Dan Guevarra, Kevin Kan, Yungchieh Lai, Ryan Jones + 5 more
Advancements in artificial intelligence (AI) for science are continually expanding the value proposition for automation in materials and chemistry experiments. The advent of hierarchical decision-making also motivates automation of not only the individual measurements but also the coordination among multiple research…