Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

Downy brome is a problematic invasive annual grass throughout western rangeland and has been increasing its abundance, spread, and impacts across Montana during the past several years. In an effort to develop effective management recommendations for control of downy brome on Montana rangeland, we compiled data from 24 trials across the state that investigated efficacy of imazapic (Plateau (R), BASF Corporation, Research Triangle Park, NC) applied at various rates and timings and with methylated seed oil (MSO) or a nonionic surfactant (NIS). We ran a mixed-model ANOVA to test for main effects and interactions across application rate (70, 105, 141, 176, and 211 g ai ha(-1)), application timing (preemergent [PRE], early postemergent [EPOST, one- to two-leaf growth stage], and postemergent [POST, three- to four-leaf growth stage]), and adjuvant (MSO, NIS). Application timing and rate interacted to affect downy brome control (P = 0.0033). PRE imazapic application resulted in the lowest downy brome control (5 to 19%), followed by POST application (25 to 77%) and EPOST application (70 to 95%). Downy brome control remained fairly consistent across rates within application timing. Adjuvant (MSO or NIS) did not affect downy brome control (P = 0.2789). Our data indicate that POST application at 105 to 141 g ai ha(-1) provides the most-consistent, short-term control of downy brome. Furthermore, applying imazapic to downy brome seedlings shortly after emergence (one- to two-leaf growth stage) provided better control than applying it to older downy brome seedlings (three- to four-leaf growth stage).

MOTIVATION:Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required.RESULTS:EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations.AVAILABILITY:The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl.CONTACT:jison@ebi.ac.uk.

The European Molecular Biology Open Software Suite (EMBOSS) is a high quality, well documented package of open source software tools for molecular biology. EMBOSS includes extensive and extensible C programming libraries, providing a powerful and robust toolkit for developing new bioinformatics tools from scratch. The EMBOSS Developer's Guide is the official and definitive guide to developing software under EMBOSS. It includes comprehensive reference information and guidelines, including step-by-step instructions and real-world code examples: • Learn how to write fully-featured tools guided by the people who developed EMBOSS • Step-by-step guide to writing EMBOSS applications, illustrated with functional, deployed code • ACD file development - learn how to customise existing tools without coding, or design and write entirely new application interfaces • EMBOSS API programming guidelines - quickly master application development • Wrapping and porting applications under EMBOSS - learn how to incorporate third-party tools

The European Molecular Biology Open Software Suite (EMBOSS) is a high quality, well documented package of open source software tools for molecular biology. EMBOSS includes extensive and extensible C programming libraries, providing a powerful and robust toolkit for developing new bioinformatics tools from scratch. The EMBOSS Developer's Manual is the official and definitive guide to developing software under EMBOSS. It includes comprehensive reference information and guidelines, including step-by-step instructions and real-world code examples: Learn how to write fully-featured tools guided by the people who developed EMBOSS Step-by-step guide to writing EMBOSS applications, illustrated with functional, deployed code ACD file development - learn how to customise existing tools without coding, or design and write entirely new application interfaces EMBOSS API programming guidelines - quickly master application development Wrapping and porting applications under EMBOSS - learn how to incorporate third-party tools

Benefits to incorporating applications into EMBOSS There are lots of good reasons for making the effort to incorporate third-party applications into EMBOSS. Just a few are listed below. Distribution It’s clearly desirable to reach as many users as possible. EMBOSS has thousands of users and many sites regularly download the latest release, so any software that’s incorporated will be widely distributed. Training cost Incorporated software is used in exactly the same way as all other EMBOSS applications. Someone familiar with EMBOSS will be able to use any application that’s been ported or wrapped. There’s no additional training requirement beyond, of course, learning about the specific methods the application implements. That is a requirement regardless of whether or not an application is in EMBOSS. Support cost Incorporated applications will benefit from a basic level of support provided by EMBOSS through the mailing lists. The level of support depends on the circumstances. An application that’s been fully ported with the understanding of it being adopted by EMBOSS would be fully supported. At the very least a user would get a reply to any email query and forwarded to where they could get more help. This is especially valuable in cases where the original author of an application has since moved away from the institute that now maintains it. Maintenance cost There might be savings on the maintenance costs. This again depends on the level of integration and the specific arrangements. At the very least EMBOSS would investigate any bugs and forward appropriate reports to the authors of the original software. There is an additional cost to maintain the port or wrapper as well as the original code, but this is more than offset by the benefits. Web services, workflows and interfaces EMBOSS has been incorporated into many graphical interfaces and workflow software such as SRS , Pipeline Pilot , Taverna , wEMBOSS and Jemboss . Further, thanks to ongoing developments in SOAPLAB , it is relatively easy to deploy an EMBOSS application as a web service. If your software is incorporated then there’s little or no additional cost in setting it up in these contexts. Database support EMBOSS supports all the common formats for input and output of sequences, sequence features and sequence alignments. Many other common data formats are supported. Any software you incorporate will be able to use these formats too. What’s more, when EMBOSS is updated to support changes to the formats, or entirely new formats, then your software will automatically benefit from these changes.

The European Molecular Biology Open Source Software Suite (EMBOSS) is the premier Open Source package of tools for molecular biology analysis and bioinformatics. Practical Bioinformatics with EMBOSS is the official and definitive guide to the package. It includes comprehensive information and practical instructions, including an in-depth tutorial and guidelines on common ways to use the package. It is written specifically for biologists, bioinformaticians and other end-users, and no prior experience with EMBOSS is assumed.

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The European Molecular Biology Open Software Suite (EMBOSS) is a high quality package of open source software tools for molecular biology. It includes over 200 applications integrated with a range of popular third party software packages under a consistent and powerful command line interface. The tools are available from a wide range of graphical interfaces, including easy to use web interfaces and powerful workflow software. The EMBOSS Administrator's Guide is the official, definitive and comprehensive guide to EMBOSS installation and maintenance: Find all the information needed to configure, install and maintain EMBOSS, including recent additions for version 6.2 Step-by-step instructions with real-world examples - saves you time and helps you avoid the pitfalls on all the common platforms In-depth reference to database configuration - learn how to set up and use databases under EMBOSS Includes EMBOSS Frequently Asked Questions (FAQ) with answers - quickly find solutions to common problems

The European Molecular Biology Open Software Suite (EMBOSS) is a high quality package of open source software tools for molecular biology. It includes over 200 applications integrated with a range of popular third party software packages under a consistent and powerful command line interface. The tools are available from a wide range of graphical interfaces, including easy to use web interfaces and powerful workflow software. The EMBOSS Administrator's Guide is the official, definitive and comprehensive guide to EMBOSS installation and maintenance: • Find all the information needed to configure, install and maintain EMBOSS, including recent additions for version 6.2 • Step-by-step instructions with real-world examples - saves readers time and helps them avoid the pitfalls on all the common platforms • In-depth reference to database configuration - learn how to set up and use databases under EMBOSS • Includes EMBOSS Frequently Asked Questions (FAQ) with answers - quickly find solutions to common problems

FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger standard, the Solexa/Illumina variants and conversion between them, based on publicly available information such as the MAQ documentation and conventions recently agreed by the Open Bioinformatics Foundation projects Biopython, BioPerl, BioRuby, BioJava and EMBOSS. Being an open access publication, it is hoped that this description, with the example files provided as Supplementary Data, will serve in future as a reference for this important file format.

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions.

BioMart Central Portal (www.biomart.org) offers a one-stop shop solution to access a wide array of biological databases. These include major biomolecular sequence, pathway and annotation databases such as Ensembl, Uniprot, Reactome, HGNC, Wormbase and PRIDE; for a complete list, visit, http://www.biomart.org/biomart/martview. Moreover, the web server features seamless data federation making cross querying of these data sources in a user friendly and unified way. The web server not only provides access through a web interface (MartView), it also supports programmatic access through a Perl API as well as RESTful and SOAP oriented web services. The website is free and open to all users and there is no login requirement.

The EMBRACE project is a network of European partners providing services which integrate the major data resources and analysis software tools using web services and emerging grid technologies. Prototype services are available for the core data resources and the most commonly used tools for sequence analysis. Data access uses the WSDbFetch and BioMart services from the European Bioinformatics Institute. Software tool services use the SoapLab services, also from the European Bioinformatics Institute. The preferred client for these services is Taverna from the myGrid project. Subprojects are collecting and analyzing biological use cases, and maintaining a watch on emerging grid technology in Europe.