1st INCF Workshop on Needs for Training in Neuroinformatics

The INCF workshop on Needs for Training in Neuroinformatics was organized by the INCF National Node of the UK. The scope of the workshop was to provide as overview of the current state of neuroinformatics training and recommendations for future provision of training. The report presents a summary of the workshop discussions and recommendations to the INCF

Libraries and the management of research data

A discussion of the role of university libraries in the management of digital research data outputs. Reviews some of the recent history of progress in this area from a UK perspective, with reference to international developments

Architectural Refactoring for Fast and Modular Bioinformatics Sequence Search

Bioinformaticists use the Basic Local Alignment Search Tool (BLAST) to characterize an unknown sequence by comparing it against a database of known sequences, thus detecting evolutionary relationships and biological properties. mpiBLAST is a widely-used, high-performance, open-source parallelization of BLAST that runs on a computer cluster delivering super-linear speedups. However, the Achilles heel of mpiBLAST is its lack of modularity, adversely affecting maintainability and extensibility; an effective architectural refactoring will benefit both users and developers. This paper describes our experiences in the architectural refactoring of mpiBLAST into a modular, high-performance software package. Our evaluation of five component-oriented designs culminated in a design that enables modularity while retaining high-performance. Furthermore, we achieved this refactoring effectively and efficiently using eXtreme Programming techniques. These experiences will be of value to software engineers faced with the challenge of creating maintainable and extensible, high-performance, bioinformatics software

Western Guide to Professional Master\u27s Programs

This guide is a resource for departments that plan to introduce new Professional Master\u27s (PMA) or Professional Science Master\u27s (PSM) degrees. The guide provides examples of existing programs, describes key criteria that new PSM programs need to meet, reviews issues in the development of new programs, and discusses the types of competencies professional programs promote in order to help their graduates compete on the job market.https://ir.lib.uwo.ca/tsc-purple-guides/1002/thumbnail.jp

Biodiversity and Biocollections: Problem of Correspondence

This text is an English translation of those several sections of the original paper in Russian, where collection-related issues are considered. The full citation of the original paper is as following: Pavlinov I.Ya. 2016. [Bioraznoobrazie i biokollektsii: problema sootvetstvia]. In: Pavlinov I.Ya. (comp.). Aspects of Biodiversity. Archives of Zoological Museum of Lomonosov Moscow State University, Vol. 54, Pр. 733–786. Orientation of biology, as a natural science, on the study and explanation of the similarities and differences between organisms led in the second half of the 20th century to the recognition of a specifi c subject area of biological explorations, viz. biodiversity (BD). One of the important general scientifi c prerequisites for this shift was understanding that (at the level of ontology) the structured diversity of the living nature is its fundamental property equivocal to subjecting of some of its manifestations to certain laws. At the level of epistemology, this led to acknowledging that the “diversifi cationary” approach to description of the living beings is as justifi able as the before dominated “unifi cationary” one. This general trend has led to a signifi cant increase in the attention to BD. From a pragmatic perspective, its leitmotif was conservation of BD as a renewable resource, while from a scientifi c perspective the leitmotif was studying it was studying BD as a specifi c natural phenomenon. These two points of view are united by recognition of the need for scientific substantiation of BD conservation strategy, which implies the need for a detailed study of BD itself. At the level of ontology, one of the key problems in the study of BD (leaving aside the question of its genesis) is determination of its structure, which is interpreted as a manifestation of the structure of the Earth’s biota itself. With this, it is acknowledged that the subject area of empirical explorations is not the BD as a whole ( “Umgebung”) but its particular manifestations (“Umwelts”). It is proposed herewith to recognized, within the latter: fragments of BD (especially taxa and ecosystems), hierarchical levels of BD (primarily within- and interorganismal ones), and aspects of BD (before all taxonomic and meronomic ones). Attention is drawn to a new interpretation of bioinformatics as a discipline that studies the information support of BD explorations. An important fraction of this support are biocollections. The scientifi c value of collections means that they make it possible both empirical inferring and testing (verification) of the knowledge about BD. This makes biocollections, in their epistemological status, equivalent to experiments, and so makes studies of BD quite scientific. It is emphasized that the natural objects (naturalia), which are permanently kept in collections, contain primary (objective) information about BD, while information retrieved somehow from them is a secondary (subjective) one. Collection, as an information resource, serves as a research sample in the studies of BD. Collection pool, as the totality of all collection materials kept in repositories according to certain standards, can be treated as a general sample, and every single collection as a local sample. The main characteristic of collection-as-sample is its representativeness; so the basic strategy of development of the collection pool is to maximize its representativeness as a means to ensure correspondence of structure of biocollection pool to that of BD itself. The most fundamental characteristic of collection, as an information resource, is its scientific signifi cance. The following three main groups of more particular characteristics are distinguished: — the “proper” characteristics of every collection are its meaningfulness, informativeness, reliability, adequacy, documenting, systematicity, volume, structure, uniqueness, stability, lability; — the “external” characteristics of collection are resolution, usability, ethic constituent; — the “service” characteristics of collection are its museofication, storage system security, inclusion in metastructure, cost. In the contemporary world, development of the biocollection pool, as a specific resource for BD research, requires considerable organizational efforts, including work on their “information support” aimed at demonstrating the necessity of existence of the biocollections