8 papers · ranked by Valyu relevance
Andrew D Yates, Jeremy Adams, Somesh Chaturvedi, Robert M. Davies + 6 more
Reference sequences are essential in creating a baseline of knowledge for many common bioinformatics methods, especially those using genomic sequencing. We have created refget, a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from…
Szymon Grabia, Ula Smyczynska, Konrad Pagacz, Wojciech Fendler
Multi-gene expression assays are an attractive tool in revealing complex regulatory mechanisms in living organisms. Normalization is an indispensable step of data analysis in all those studies, since it removes unwanted, non-biological variability from data. In targeted qPCR assays the normalization is typically…
Zakaria Mehrab, Jaiaid Mobin, Ibrahim Asadullah Tahmid, Atif Rahman
Genome wide association studies (GWAS) attempt to map genotypes to phenotypes in organisms. This is typically performed by genotyping individuals using microarray or by aligning whole genome sequencing reads to a reference genome. Both approaches require knowledge of a reference genome which limits their application to…
Duc Nguyen, Erin L. Rich, Joni D. Wallis, Kenway Louie + 1 more
The decisional reference point serves as a hidden benchmark for evaluating options in decision-making. Despite extensive behavioral evidence for the existence of the reference point, its neural instantiation remains unclear. To identify reference point encoding at both the single-neuron and population levels, we…
James K Bonfield
The reference CRAM file format implementation is in Java. We present “Scramble”: a new C implementation of SAM, BAM and CRAM file I/O. The C API for CRAM is 1.5–1.7x slower than BAM at decoding, but 1.8–2.6x faster at encoding. We see file size savings of 40–50%. Source code is available from…
George Dimitriadis, Ella Svahn, Andrew MacAskill, Athena Akrami
To realise a research project idea, an experimenter faces a series of conflicting design and implementation considerations, regarding both its hardware and software components. For instance, the ease of implementation, in time and expertise, should be balanced against the ease of future reconfigurability and number of…
Semen Yesylevskyy
Transition to the memory safe natively compiled programming languages is a major software development trend in recent years, which eliminates memory-related security exploits, enables a fearless concurrency and parallelization, and drastically improves ergonomics and speed of software development. Modern memory-safe…
Sabine U. König, Caspar Goeke, Tobias Meilinger, Peter König
Theories of Enactivism propose an action-oriented approach to understand human cognition. So far, however, empirical evidence supporting these theories has been sparse. Here, we investigate whether spatial navigation based on allocentric reference frames that are independent of the observer’s physical body can be…