15 papers · ranked by Valyu relevance
Jose L Figueroa, Richard Allen White
We now exist in the era of massive datasets from genomics, large language models, and all the known knowledge of humanity right at our fingertips. Much of this data is becoming more accessible; however, processing such data remains an ongoing issue across systems including high performance computing (HPC)…
Seth Stadick
Filtering records using command line tools is a staple of Bioin-formatics. In analysis pipelines and in day-to-day research tools such as awk, grep, and cut are the workhorses of much of our data crunching. To date, there is no command line utility for performing index-free alignment-based filtering of records. Ish is…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread…
Debaleena Basu, Naveen Sendhilnathan, Aditya Murthy
A ramp to threshold activity of frontal Eye Field (FEF) movement-related neurons best explains the reaction time of single saccades. How such activity is modulated by a concurrent saccade plan is not known. Borrowing from psychological theories of capacity sharing that are designed to explain the concurrent planning of…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
John M Macdonald, Christopher M Lalansingh, Christopher I Cooper, Anqi Yang + 2 more
Most biocomputing pipelines are run on clusters of computers. Each type of cluster has its own API (application programming interface). That API defines how a program that is to run on the cluster must request the submission, content and monitoring of jobs to be run on the cluster. Sometimes, it is desirable to run the…
Raja Appuswamy, Jacques Fellay, Nimisha Chaturvedi
Rapid advances in sequencing technologies are producing genomic data on an unprecedented scale. The first, and often one of the most time consuming, step of genomic data analysis is sequence alignment, where sequenced reads must be aligned to a reference genome. Several years of research on alignment algorithms has led…
Authors not listed
Background: Pharmaceutical batch scheduling in multi-reactor configurations presents complex optimization challenges under operational uncertainty, yet limited research addresses how parallel processing capacity affects heuristic performance and predictive modeling. Objectives: This study investigated scheduling…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
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…
Aaron Liu, Myeongyeon Lee, Rahul Venkatesh, Jessica Bonsu + 4 more
Polymer-based semiconductors and organic electronics encapsulate a significant research thrust for informatics-driven materials development. However, device measurements are described by a complex array of design and parameter choices, many of which are sparsely reported. For example, the mobility of a polymer-based…
Authors not listed
This paper presents GLAS (Git-based Lab Automated Scheduler or Get Lab Automation Simplified), an open-source, robust, and highly expandable Git-based architecture designed for laboratory automation. GLAS can be deployed in both partially and fully automated experimental science laboratories, enabling the development…
Authors not listed
The exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions…
Authors not listed
Automated chemistry platforms hold the potential to enable large-scale organic synthesis campaigns, such as producing a library of compounds for biological evaluation. The efficiency of such platforms will depend on the schedule according to which the synthesis operations are executed. In this work, we study the…