11 papers · ranked by Valyu relevance
Mehmet Aziz Yirik, Maria Sorokina, Christoph Steinbeck
The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of…
Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the…
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…
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…
Łukasz Szeremeta
The use of computers to store and process different types of data is growing every day. The same applies to chemical data. SDF and Open Babel are recognized solutions in this field. However, each solution has its drawbacks, which are revealed in specific applications. It is important to be able to easily convert the…
Mehmet Aziz Yirik, Maria Sorokina, Christoph Steinbeck
The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of…
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…
Felix Bänsch, Jonas Schaub, Betül Sevindik, Samuel Behr + 3 more
Developing and implementing computational algorithms for the extraction of specific substructures from molecular graphs (in silico molecule fragmentation) is an iterative process. It involves repeated sequences of implementing a rule set, applying it to relevant structural data, checking the results, and adjusting the…
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…