12 papers · ranked by Valyu relevance
Pierre Lindenbaum, Matilde Karakachoff, Richard Redon
Visualizing BAM and VCF files is a common task for biologists, but they’re missing a way to filter and to explore the details of each short-read or variation. In that context, we wrote an interactive java-based interface named JfxNgs that uses javascript snippets to filter and reformat BAM and VCF files.…
Costanza Pascal, Herzeel Charlotte, Verachtert Wilfried
elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file for multiple preparation steps, and keeps sequencing data as much as possible in main memory. Similar to other…
Rafael Bravo, Mark Robertson-Tessi, Alexander R. A. Anderson
The Hybrid Automata Library (HAL) is a Java Library made of simple, efficient, generic components that can be used to model complex spatial systems. HAL’s components can broadly be classified into: on- and off-lattice agent containers, finite difference diffusion fields, a Gui building system, and additional tools and…
O. Frank Huffman, Aart W.J. Berkhout, Paul C.H. Albers, John de Vos + 1 more
The scientific utility of Eugène Dubois’ Pithecanthropus erectus (P.e.) Skullcap (Trinil 1), Femur I (Trinil 3) and associated paleontological specimens has been impaired for over a century by questions about their provenience. Firsthand accounts and contemporaneous field photographs, presented here, extensively…
Rebecca N Lewis, Anthony Kwong, Masayo Soma, Selvino R de Kort + 1 more
Linguistic laws, which describe common statistical patterns in human language, are often studied in animal communication systems. Despite good evidence for adherence to these laws in non-human primate communication, there is still a paucity of data on other taxa. Birdsong is often used as a model for human language…
Sota Kikuchi, Noriko Kondo, Hiroki Koda
Vocal exchange or turn-taking - an interaction in which vocalizer alternation occurs at very short intervals to avoid overlapping vocalizations - occurs not only in human conversation but also in animal communications, characterized by temporal regularities in the timing of spontaneous and response vocalizations. This…
John C. Bowler, George Zakka, Hyun Choong Yong, Wenke Li + 4 more
Investigators conducting behavioral experiments often need precise control over the timing of the delivery of stimuli to subjects and to collect the precise times of the subsequent behavioral responses. Furthermore, investigators want fine-tuned control over how various multi-modal cues are presented. behaviorMate…
Andri Wibowo
The milky sea is one of the unique natural phenomena caused by the presence of luminous Vibrio bacteria in marine ecosystems. Recently a milky sea has been reported frequently included in the Java Southern Sea. Simultaneously, numerous remote sensing based approaches have been developed to detect the presence of…
Rebecca N. Lewis, Hiroharu Makioka, R. Tucker Gilman, Masayo Soma
Songs play an important role in mate choice for a range of bird species. Many female birds show preferences for specific song features, such as complexity and temporal characteristics, or song familiarity. These features may indicate male quality, or help females to identify locally adapted or genetically compatible…
Samuel Vanden Abeele, Steven B. Janssens, Justin Asimonyio Anio, Yves Bawin + 7 more
Many cultivated coffee varieties descend from Coffea canephora, commonly known as Robusta coffee. The Congo Basin has a century long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic…
Lauren Verleysen, Robrecht Bollen, Jean-Léon Kambale, Ebele Tshimi + 8 more
Cultivation of Robusta coffee is likely to gain importance because of its high disease resistance and climate envelope, but substantial effort must be made to improve its cupping quality and other agronomic traits. Robusta coffee genetic resources conserved in field genebanks can play an important role in this context…
Chinyere F. Anagbogu, Jiaqi Zhou, Festus O. Olasupo, Mohammed Baba-Nitsa + 1 more
Coffee (Coffea spp.) is one of the most popular refreshments globally. Coffee lipid diversity has untapped potential for improving coffee marketability because lipids contribute significantly to both the health benefits and cup quality of coffee. However, there have not been extensive studies of lipids of C. canephora…