ENCODE data at the ENCODE portal.

The Encyclopedia of DNA Elements (ENCODE) Project is in its third phase of creating a comprehensive catalog of functional elements in the human genome. This phase of the project includes an expansion of assays that measure diverse RNA populations, identify proteins that interact with RNA and DNA, probe regions of DNA hypersensitivity, and measure levels of DNA methylation in a wide range of cell and tissue types to identify putative regulatory elements. To date, results for almost 5000 experiments have been released for use by the scientific community. These data are available for searching, visualization and download at the new ENCODE Portal (www.encodeproject.org). The revamped ENCODE Portal provides new ways to browse and search the ENCODE data based on the metadata that describe the assays as well as summaries of the assays that focus on data provenance. In addition, it is a flexible platform that allows integration of genomic data from multiple projects. The portal experience was designed to improve access to ENCODE data by relying on metadata that allow reusability and reproducibility of the experiments.

The Influence of Training Age on the Annual Development of Physical Qualities Within Academy Rugby League Players.

Till, K, Darrall-Jones, J, Weakley, JJ, Roe, GA, and Jones, BL. The influence of training age on the annual development of physical qualities within academy rugby league players. J Strength Cond Res 31(8): 2110-2118, 2017-Previous research in academy rugby league players has evaluated the development of physical qualities according to chronological age. However, no study has considered the training age, defined as the number of formalized years of strength and conditioning training, of these players. Therefore, the purpose of this study was to present and compare the annual changes in physical qualities of academy rugby league players according to training age. Sixty-one academy players undertook a fitness testing assessment, including anthropometric (height, body mass, sum of 4 skinfolds) and physical (10 and 20 m sprint, 10m momentum, vertical jump, Yo-Yo intermittent recovery test level 1 [Yo-Yo IRTL1], one-repetition maximum [1RM] squat, bench press and prone row) measures at the start of preseason on 2 consecutive annual occasions. Players were categorized into one of 3 training age groups (i.e., 0, 1, or 2 years) and were analyzed using magnitude-based inferences. Almost certain, very likely or likely annual improvements were identified for body mass, 10m momentum, Yo-Yo IRTL1, vertical jump, and all strength measures for the 3 training age groups. When training age groups were compared, 1 year showed possibly or likely lower strength increases than 0 years training age. However, the 2 years training age group demonstrated possibly or likely increased strength changes compared with 1 year. These findings suggest that training age is an important consideration for strength and conditioning practitioners but it is likely to be a combination of chronological age, biological maturity, and training experience alongside dynamic interplayer variability that influences the physical development of academy rugby league players.

Saccharomyces genome database provides new regulation data.

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the community resource for genomic, gene and protein information about the budding yeast Saccharomyces cerevisiae, containing a variety of functional information about each yeast gene and gene product. We have recently added regulatory information to SGD and present it on a new tabbed section of the Locus Summary entitled 'Regulation'. We are compiling transcriptional regulator-target gene relationships, which are curated from the literature at SGD or imported, with permission, from the YEASTRACT database. For nearly every S. cerevisiae gene, the Regulation page displays a table of annotations showing the regulators of that gene, and a graphical visualization of its regulatory network. For genes whose products act as transcription factors, the Regulation page also shows a table of their target genes, accompanied by a Gene Ontology enrichment analysis of the biological processes in which those genes participate. We additionally synthesize information from the literature for each transcription factor in a free-text Regulation Summary, and provide other information relevant to its regulatory function, such as DNA binding site motifs and protein domains. All of the regulation data are available for querying, analysis and download via YeastMine, the InterMine-based data warehouse system in use at SGD.

The UCSC Genome Browser database: extensions and updates 2013.

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

The UCSC Genome Browser database: extensions and updates 2011.

The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011. Further, a large number of annotation tracks have been either added, updated by contributors, or remapped to the latest human reference genome. Among these are new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods. Growing beyond the local database, this year we have introduced 'track data hubs', which allow the Genome Browser to provide access to remotely located sets of annotations. This feature is designed to significantly extend the number and variety of annotation tracks that are publicly available for visualization and analysis from within our site. We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image.

Applied Sport Science for Male Age-Grade Rugby Union in England.

Rugby union (RU) is a skill-collision team sport played at junior and senior levels worldwide. Within England, age-grade rugby governs the participation and talent development of youth players. The RU player development pathway has recently been questioned, regarding player performance and well-being, which sport science research can address. The purpose of this review was to summarise and critically appraise the literature in relation to the applied sport science of male age-grade RU players in England focussing upon (1) match-play characteristics, (2) training exposures, (3) physical qualities, (4) fatigue and recovery, (5) nutrition, (6) psychological challenges and development, and (7) injury. Current research evidence suggests that age, playing level and position influence the match-play characteristics of age-grade RU. Training exposures of players are described as 'organised chaos' due to the multiple environments and stakeholders involved in coordinating training schedules. Fatigue is apparent up to 72 h post match-play. Well-developed physical qualities are important for player development and injury risk reduction. The nutritional requirements are high due to the energetic costs of collisions. Concerns around the psychological characteristics have also been identified (e.g. perfectionism). Injury risk is an important consideration with prevention strategies available. This review highlights the important multi-disciplinary aspects of sport science for developing age-grade RU players for continued participation and player development. The review describes where some current practices may not be optimal, provides a framework to assist practitioners to effectively prepare age-grade players for the holistic demands of youth RU and considers areas for future research.

The Effects of Augmented Feedback on Sprint, Jump, and Strength Adaptations in Rugby Union Players After a 4-Week Training Program.

PURPOSE: Feedback can enhance acute physical performance. However, its effects on physical adaptation have received little attention. Therefore, the purpose of this study was to determine the effect of feedback during a 4-wk training program on jump, sprint, and strength adaptations. METHODS: A total of 28 semiprofessional male rugby union players were strength-matched into 2 groups (feedback and nonfeedback). During the 4-wk training program, the Feedback group received immediate, objective feedback on (1) mean concentric velocity during resistance training repetitions, (2) distance feedback for standing broad jumps, and (3) time for sprints. The Nonfeedback group was not provided additional information. Across the 4-wk mesocycle, subjects completed 3 strength and conditioning sessions per week. Countermovement jump, standing long jump, 10- and 20-m sprint, and 3-repetition-maximum barbell back squat and bench press were measured before and after the training intervention. Magnitude-based inferences assessed meaningful changes within and between groups. RESULTS: The Feedback group showed small to moderate improvements in outcome measures, whereas the Nonfeedback group demonstrated trivial to small improvements. Improvements in countermovement-jump relative peak power (effect size ± 90% confidence limits: 0.34 ± 0.42), 10-m (0.20 ± 0.35) and 20-m sprints (0.40 ± 0.21), and 3-repetition-maximum back squats (0.23 ± 0.17) were possibly to likely greater for the Feedback condition than for Nonfeedback. CONCLUSIONS: Providing augmented feedback during strength and conditioning routines can enhance training adaptations compared with athletes who do not receive feedback. Consequently, practitioners should consider providing kinematic outputs, displacement, or sprint time at the completion of each repetition as athletes train.

The Physical Characteristics of Specific Phases of Play During Rugby Union Match Play.

PURPOSE: To quantify the frequencies and timings of rugby union match-play phases (ie, attacking, defending, ball in play [BIP], and ball out of play [BOP]) and then compare the physical characteristics of attacking, defending, and BOP between forwards and backs. METHODS: Data were analyzed from 59 male rugby union academy players (259 observations). Each player wore a microtechnology device (OptimEye S5; Catapult, Melbourne, Australia) with video footage analyzed for phase timings and frequencies. Dependent variables were analyzed using a linear mixed-effects model and assessed with magnitude-based inferences and Cohen d effect sizes (ES). RESULTS: Attack, defense, BIP, and BOP times were 12.7 (3.1), 14.7 (2.5), 27.4 (2.9), and 47.4 (4.1) min, respectively. Mean attack (26 [17] s), defense (26 [18] s), and BIP (33 [24] s) phases were shorter than BOP phases (59 [33] s). The relative distance in attacking phases was similar (112.2 [48.4] vs 114.6 [52.3] m·min-1, ES = 0.00 ± 0.23) between forwards and backs but greater in forwards (114.5 [52.7] vs 109.0 [54.8] m·min-1, ES = 0.32 ± 0.23) during defense and greater in backs during BOP (ES = -0.66 ± 0.23). CONCLUSIONS: Total time in attack, defense, and therefore BIP was less than BOP. Relative distance was greater in forwards during defense, whereas it was greater in backs during BOP and similar between positions during attack. Players should be exposed to training intensities from in-play phases (ie, attack and defense) rather than whole-match data and practice technical skills during these intensities.

Principles of metadata organization at the ENCODE data coordination center.

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center (DCC) is responsible for organizing, describing and providing access to the diverse data generated by the ENCODE project. The description of these data, known as metadata, includes the biological sample used as input, the protocols and assays performed on these samples, the data files generated from the results and the computational methods used to analyze the data. Here, we outline the principles and philosophy used to define the ENCODE metadata in order to create a metadata standard that can be applied to diverse assays and multiple genomic projects. In addition, we present how the data are validated and used by the ENCODE DCC in creating the ENCODE Portal (https://www.encodeproject.org/). Database URL: www.encodeproject.org.