Integrating sequence and structural biology with DAS.

BACKGROUND: The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. RESULTS: Here we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources. CONCLUSION: Our DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at http://www.dasregistry.org.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Ensembl’s 10th year

Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide complete gene annotations for all supported species in addition to specific resources that target genome variation, function and evolution. Ensembl data is accessible in a variety of formats including via our genome browser, API and BioMart. This year marks the tenth anniversary of Ensembl and in that time the project has grown with advances in genome technology. As of release 56 (September 2009), Ensembl supports 51 species including marmoset, pig, zebra finch, lizard, gorilla and wallaby, which were added in the past year. Major additions and improvements to Ensembl since our previous report include the incorporation of the human GRCh37 assembly, enhanced visualisation and data-mining options for the Ensembl regulatory features and continued development of our software infrastructure

Integrating sequence and structural biology with DAS.

BACKGROUND: The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence. RESULTS: Here we present several extensions to the current DAS 1.5 protocol. These provide new commands to share alignments, three dimensional molecular structure data, add the possibility for registration and discovery of DAS servers, and provide a convention how to provide different types of data plots. We present examples of web sites and applications that use the new extensions. We operate a public registry of DAS sources, which now includes entries for more than 250 distinct sources. CONCLUSION: Our DAS extensions are essential for the management of the growing number of services and exchange of diverse biological data sets. In addition the extensions allow new types of applications to be developed and scientific questions to be addressed. The registry of DAS sources is available at http://www.dasregistry.org.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Hearing health - an online hearing loss prevention program

https://www.internetaudiology.com/2021/?p=presentation

The development and evaluation of an online hearing loss prevention program

Recent studies underline the need for research on approaches to encouraging healthy listening habits. This study aims to develop and evaluate an online hearing loss prevention program; and examine its influence on the participants’ use of hearing protection, hearing loss prevention knowledge, attitude towards noise, and program useability and adherence.The study was conducted in the county of Västra Götaland, Sweden, from March through October 2021. The program included four modules focused on hearing and hearing loss prevention and was accessible to the participants for four weeks. In total, 75 participants completed the program which was evaluated using the Youth Attitude to Noise Scale and four additional self-designed questionnaires. The questionnaires were deployed before and immediately after program completion.The findings indicate that the program may influence the participants’ attitudes toward noise and the use of hearing protection. The participants who completed the program perceived high useability and increased hearing loss prevention knowledge. This program is most needed to promote healthy hearing. Future studies should target specific groups with this program and evaluate its long-term effects

biodiversitydata-se/mol-mod: Simplified backup

<p>In this release, we primarily: • Simplify the backup procedure in scheduled-backup.sh. This script was initially designed to both copy data from containers to the host, and to rsync to another machine. However, in the current (SBDI) context, it makes more sense to simply copy data and logs to a single /backups directory, from where they are then rsynced to the central backup by external scripts.</p> <p>We also: • Update a few dependencies (urlib, werkzeug and Flask-WTF) as prompted by Dependabot. • Change the styling av result tables so that bottom info on selections and filters etc. doesn't collide with pagination element.</p&gt

We are providing a convention how to configure the display of different data-plots via the DAS stylesheet command

<p><b>Copyright information:</b></p><p>Taken from "Integrating sequence and structural biology with DAS"</p><p>http://www.biomedcentral.com/1471-2105/8/333</p><p>BMC Bioinformatics 2007;8():333-333.</p><p>Published online 12 Sep 2007</p><p>PMCID:PMC2031907.</p><p></p> Here an example how this is used for plotting the scores of the signal peptide and transmembrane topology predictor Phobius [48], as well as hydropathicity data for the Suppressor of tumorigenicity protein 14 (Q9Y5Y6). The DAS features used in the three displays are exactly the same. The configuration is obtained from the stylesheet responses. The example can be also viewed via [49]. A) Using the stylesheet for histogram display. B) Using the stylesheet for lineplot display. C) Using the stylesheet for gradient display

NBISweden/wgs-structvar: 1.1.3

Whole Genome Sequenceing Structural Variation Pipeline

Integrating biological data--the Distributed Annotation System

BACKGROUND: The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics. RESULTS: Here we describe the various infrastructure components of DAS and present a new extended version of the DAS specification. Version 1.53E incorporates several recent developments, including its extension to serve new data types and an ontology for protein features. CONCLUSION: Our extensions to the DAS protocol have facilitated the integration of new data types, and our improvements to the existing DAS infrastructure have addressed recent challenges. The steadily increasing numbers of available data sources demonstrates further adoption of the DAS protocol