This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been-so far-no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies.

Sustainable noncommercial bioinformatics infrastructures are a prerequisite to use and take advantage of the potential of big data analysis for research and economy. Consequently, funders, universities and institutes as well as users ask for a transparent value model for the tools and services offered. In this article, a generally applicable lightweight method is described by which bioinformatics infrastructure projects can estimate the value of tools and services offered without determining exactly the total costs of ownership. Five representative scenarios for value estimation from a rough estimation to a detailed breakdown of costs are presented. To account for the diversity in bioinformatics applications and services, the notion of service-specific 'service provision units' is introduced together with the factors influencing them and the main underlying assumptions for these 'value influencing factors'. Special attention is given on how to handle personnel costs and indirect costs such as electricity. Four examples are presented for the calculation of the value of tools and services provided by the German Network for Bioinformatics Infrastructure (de.NBI): one for tool usage, one for (Web-based) database analyses, one for consulting services and one for bioinformatics training events. Finally, from the discussed values, the costs of direct funding and the costs of payment of services by funded projects are calculated and compared.

SUMMARY The increase in volume and complexity of biological data has led to increased requirements to reuse that data. Consistent and accurate metadata is essential for this task, creating new challenges in semantic data annotation and in the constriction of terminologies and ontologies used for annotation. The BioSharing community are developing standards and terminologies for annotation, which have been adopted across bioinformatics, but the real challenge is to make these standards accessible to laboratory scientists. Widespread adoption requires the provision of tools to assist scientists whilst reducing the complexities of working with semantics. This paper describes unobtrusive ‘stealthy’ methods for collecting standards compliant, semantically annotated data and for contributing to ontologies used for those annotations. Spreadsheets are ubiquitous in laboratory data management. Our spreadsheet‐based RightField tool enables scientists to structure information and select ontology terms for annotation within spreadsheets, producing high quality, consistent data without changing common working practices. Furthermore, our Populous spreadsheet tool proves effective for gathering domain knowledge in the form of Web Ontology Language (OWL) ontologies. Such a corpus of structured and semantically enriched knowledge can be extracted in Resource Description Framework (RDF), providing further means for searching across the content and contributing to Open Linked Data ( http://linkeddata.org/ ). Copyright © 2012 John Wiley & Sons, Ltd.

The interpretation and integration of experimental data depends on consistent metadata and uniform annotation. However, there are many barriers to the acquisition of this rich semantic metadata, not least the overhead and complexity of its collection by scientists. We present RightField, a lightweight spreadsheet-based annotation tool for lowering the barrier of manual metadata acquisition; and a data integration application for extracting and querying RDF data from these enriched spreadsheets. By hiding the complexities of semantic annotation, we can improve the collection of rich metadata, at source, by scientists. We illustrate the approach with results from the SysMO program, showing that RightField supports the whole workflow of semantic data collection, submission and RDF querying in Systems Biology. The RightField tool is freely available from http://www.rightfield.org.uk, and the code is open source under the BSD License.

MOTIVATION: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, may have little experience in the use of such standards and require tools to support this form of data annotation. RESULTS: RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets. Individual cells, columns or rows can be restricted to particular ranges of allowed classes or instances from chosen ontologies. The RightField-enabled spreadsheet presents selected ontology terms to the users as a simple drop-down list, enabling scientists to consistently annotate their data. The result is 'semantic annotation by stealth', with an annotation process that is less error-prone, more efficient, and more consistent with community standards. AVAILABILITY AND IMPLEMENTATION: RightField is open source under a BSD license and freely available from http://www.rightfield.org.uk

SUMMARY: The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2L(A)T(E)X, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, L(A)T(E)X and PDF, and provides many settings for customization. AVAILABILITY: Source code, documentation and a web service are freely available at (http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX).

In peer-to-peer (P2P) networks, computers with equal rights form a logical (overlay) network in order to provide a common service that lies beyond the capacity of every single participant. Efficient similarity search is generally recognized as a frontier in research about P2P systems. One way to address it is using data source selection based approaches where peers summarize the data they contribute to the network, generating typically one summary per peer. When processing queries, these summaries are used to choose the peers (data sources) that are most likely to contribute to the query result. Only those data sources are contacted. There are two main contributions of this paper. We extend earlier work, adding a data source selection method for high-dimensional vector data, comparing different peer ranking schemes. More importantly, we present a method that uses progressive stepwise data exchange between peers to better each peer's summary and therefore improve the system's performance

Given some of the recent advances in distributed hash table (DHT) based peer-to-peer (P2P) systems we ask the following questions: are there applications where unstructured queries are still necessary (i.e., the underlying queries do not efficiently map onto any structured framework), and are there unstructured P2P systems that can deliver the high bandwidth and computing performance necessary to support such applications. Toward this end, we consider an image search application which supports queries based on image similarity metrics, such as color histogram intersection, and discuss why in this setting, standard DHT approaches are not directly applicable. We then study the feasibility of implementing such an image search system on two different unstructured P2P systems: power-law topology with percolation search, and an optimized super-node topology using structured broadcasts. We examine the average and maximum values for node bandwidth, storage and processing requirements in the percolation and super-node models, and show that current high-end computers and high-speed links have sufficient resources to enable deployments of large-scale complex image search systems

Much of the present P2P-IR literature is focused on distributed indexing structures. Within this paper, we present an approach based on the replication of peer data summaries via rumor spreading and multicast in a structured overlay.We will describe Rumorama, a P2P framework for similar-ity queries inspired by GlOSS and CORI and their P2P-adaptation, PlanetP. Rumorama achieves a hierarchization of PlanetP-like summary-based P2P-IR networks. In a Rumorama network, each peer views the network as a small PlanetP network with connections to peers that see other small PlanetP networks. One important aspect is that each peer can choose the size of the PlanetP network it wants to see according to its local processing power and bandwidth. Even in this adaptive environment, Rumorama manages to process a query such that the summary of each peer is considered exactly once in a network without churn. However, the actual number of peers to be contacted for a query is a small fraction of the total number of peers in the network.Within this article, we present the Rumorama base protocol, as well as experiments demonstrating the scalability and viability of the approach under churn.

Benchmarking has always been a crucial problem in content-based image retrieval (CBIR). A key issue is the lack of a common access method to retrieval systems, such as SQL for relational databases. The Multimedia Retrieval Mark-up Language (MRML) solves this problem by standardizing access to CBIR systems (CBIRSs). Other difficult problems are also shortly addressed, such as obtaining relevance judgments and choosing a database for performance comparison. In this article we present a fully automated benchmark for CBIRSs based on MRML, which can be adapted to any image database and almost any kind of relevance judgment. The test evaluates theperformance of positive and negative relevance feedback, which can be generated automatically from the relevance judgments. To illustrate our purpose, a freely available, non-copyright image collection is used to evaluate our CBIRS, Viper. All scripts described here are also freely available for download.

Abstract In this article we address the problem of benchmarking image browsers. Image browsers are systems that help the user in finding an image from scratch, as opposed to query by example (QBE), where an example image is needed. The existence of different search paradigms for image browsers makes it difficult to compare image browsers. Currently, the only admissible way of evaluation is by conducting large‐scale user studies. This makes it difficult to use such an evaluation as a tool for improving browsing systems. As a solution, we propose an automatic image browser benchmark that uses structured text annotation of the image collection for the simulation of the user's needs. We apply such a benchmark on an example system.

Relevance feedback has been shown to be a very effective tool for enhancing retrieval results in text retrieval. It has also been increasingly used in content-based image retrieval and very good results have been obtained. However, too much negative feedback may destroy a query as good features get negative weightings. This paper compares a variety of strategies for positive and negative feedback. The performance evaluation of feedback algorithms is a hard problem. To solve this, we obtain judgments from several users and employ an automated feedback scheme. We then evaluate different techniques using the same judgements. Using automated feedback, the ability of a system to adapt to the user's needs can be measured very effectively. Our study highlights the utility of negative feedback, especially over several feedback steps.