10 papers · ranked by Valyu relevance
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.…
Weimin Zhang, Luciana Lazar-Stefanita, Hitoyoshi Yamashita, Michael J. Shen + 61 more
Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp Saccharomyces…
Shreyansh Agrawal, Harsh B. Anadkat, Kiran K. Athimoolam, Harsh Bhardwaj + 8 more
Recent advances in artificial intelligence (AI) have prompted claims about autonomous “AI scientists,” yet systematic evaluations of these capabilities remain scarce. This exploratory study investigates whether current AI frameworks can execute scientific research tasks beyond isolated demonstrations. We tested eight…
Fernando Cruz, João Capela, Eugénio C. Ferreira, Miguel Rocha + 1 more
As the reconstruction of Genome-Scale Metabolic Models becomes standard practice in systems biology, the number of organisms having at least one metabolic model at the genome-scale is peaking at an unprecedented scale. The automation of several laborious tasks, such as gap-finding and gap-filling, allowed to develop…
Christopher Schölzel, Valeria Blesius, Gernot Ernst, Alexander Goesmann + 1 more
One should assume that in silico experiments in systems biology are less susceptible to reproducibility issues than their wet-lab counterparts, because they are free from natural biological variations and their environment can be fully controlled. However, recent studies show that only half of the published…
Sana Gul, Rizwan Bin Faiz, Mohammad Aljaidi, Ghassan Samara + 2 more
Cross-project defect prediction (CPDP) is a significant way of defect identification in the project. In cross-project defect prediction, we extract knowledge from the source project and apply that learned knowledge to predict labels for the target project. However, the model performance can be affected by features that…
Sergi Valverde, Manuel Porcar, Juli Peretó, Ricard V. Solé
In fifteen years, Synthetic Biology (SB) has moved from proof-of-concept designs to several flagship achievements. Standardisation efforts are still under way, basic engineering concepts such as modularity and orthogonality are still controversial in biology, and making predictions from computer models is still…
Azza E. Ahmed, Jacob Heldenbrand, Yan Asmann, Faisal M. Fadlelmola + 10 more
Genomic variant discovery is frequently performed using the GATK Best Practices variant calling pipeline, a complex workflow with multiple steps, fans/merges, and conditionals. This complexity makes management of the workflow difficult on a computer cluster, especially when running in parallel on large batches of data…
Paul P. Gardner, James M. Paterson, Fatemeh Ashari-Ghomi, Sinan U. Umu + 2 more
Computational biology has provided widely used and powerful software tools for testing and making inferences about biological data. In the face of increasing volumes of data, heuristic methods that trade software speed for mathematical completeness must be employed. We are interested in whether trade-offs between speed…
Mikkel D. Andreasen, Paulo C. T. Souza, Birgit Schiøtt, Lorena Zuzic
Current trends in molecular modelling are geared towards increasingly realistic representations of the modelled systems. This is reflected in larger, more complex systems, which are difficult to build and would ideally rely on a software that converts userprovided descriptors into system coordinates. This is not a…