9 papers · ranked by Valyu relevance
Marco Enrico Piras, Luca Pireddu, Gianluigi Zanetti
Workflow managers for scientific analysis provide a high-level programming platform facilitating standardization, automation, collaboration and access to sophisticated computing resources. The Galaxy workflow manager provides a prime example of this type of platform. As compositions of simpler tools, workflows…
Lukas Forer, Sebastian Schönherr
The workflow management system Nextflow builds together with the nf-core community an essential ecosystem in Bioinformatics. However, ensuring the correctness and reliability of large and complex pipelines is challenging, since a unified and automated unit-style testing framework specific to Nextflow is still missing.…
Alberto Florez Prada, Darren J. Hart
Validating bioinformatics pipelines and benchmarking sequence processing algorithms requires reliable test datasets. Existing read simulation tools rely on reference genomes and empirical error profiles, lacking fine-grained control over specific targeted DNA constructs and controlled error injection.…
Wenhui Sophia Lu, Xiaowei Zhang, Luis S. Mille-Fragoso, Haoyu Dai + 2 more
Engineering protein variants to function in exogenous environments remains a significant challenge due to the complexity of sequence and fitness landscapes. Experimental strategies often require extensive labor and domain expertise. While recent advances in protein generative modeling offer a promising in silico…
Alexander C. Reis, Howard M. Salis
Gene expression models greatly accelerate the engineering of synthetic metabolic pathways and genetic circuits by predicting sequence-function relationships and reducing trial-and-error experimentation. However, developing models with more accurate predictions is a significant challenge, even though they are essential…
Chin Jian Yang, Rodney N. Edmondson, Hans-Peter Piepho, Wayne Powell + 1 more
Multiparental advanced generation inter-cross (MAGIC) populations are valuable crop resources with a wide array of research uses including genetic mapping of complex traits, management of genetic resources and breeding of new varieties. Multiple founders are crossed to create a rich mosaic of highly recombined founder…
Bryan Glazer, Jonathan Lifferth, Carlos F. Lopez
Many important processes in biology, such as signaling and gene regulation, can be described using logic models. These logic models are typically built to behaviorally emulate experimentally observed phenotypes, which are assumed to be steady states of a biological system. Most models are built by hand and therefore…
Christian Carsten Sachs, Karina Ruzaeva, Johannes Seiffarth, Wolfgang Wiechert + 2 more
To address the need for ground truth data for deep learning based segmentation algorithms in microfluidic live-cell imaging, we present CellSium, a cell simulator primarily aimed at synthesizing realistic image sequences of bacterial microcolonies suitable for training neural networks. CellSium is free and open source…
Ihsan Tolga Medeni, Metehan Ünal, Roberto Galizi, Bryan Bartley + 4 more
Large language models have transformed software engineering practices. However, generated artefacts are not always developer-friendly and may partially meet complex requirements. As the need to standardise, integrate, and develop tools in engineering biology increases, novel approaches are needed to create and maintain…