Gustavo A. Salazar

The Pfam protein families database: towards a more sustainable future

In the last two years the Pfam database (http://pfam.xfam.org) has undergone a substantial reorganisation to reduce the effort involved in making a release, thereby permitting more frequent releases. Arguably the most significant of these changes is that Pfam is now primarily based on the UniProtKB reference proteomes, with the counts of matched sequences and species reported on the website restricted to this smaller set. Building families on reference proteomes sequences brings greater stability, which decreases the amount of manual curation required to maintain them. It also reduces the number of sequences displayed on the website, whilst still providing access to many important model organisms. Matches to the full UniProtKB database are, however, still available and Pfam annotations for individual UniProtKB sequences can still be retrieved. Some Pfam entries (1.6%) which have no matches to reference proteomes remain; we are working with UniProt to see if sequences from them can be incorporated into reference proteomes. Pfam-B, the automatically-generated supplement to Pfam, has been removed. The current release (Pfam 29.0) includes 16 295 entries and 559 clans. The facility to view the relationship between families within a clan has been improved by the introduction of a new tool.

BioJS: an open source JavaScript framework for biological data visualization.

SUMMARY BioJS is an open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It follows a community-driven standard specification that includes a collection of components purposely designed to require a very simple configuration and installation. In addition to the programming framework, BioJS provides a centralized repository of components available for reutilization by the bioinformatics community. AVAILABILITY AND IMPLEMENTATION http://code.google.com/p/biojs/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Dasty2, an Ajax protein DAS client

SUMMARY Dasty2 is a highly interactive web client integrating protein sequence annotations from currently more than 40 sources, using the distributed annotation system (DAS). AVAILABILITY Dasty2 is an open source tool freely available under the terms of the Apache License 2.0, publicly available at http://www.ebi.ac.uk/dasty/.

BioJS: an open source standard for biological visualisation - its status in 2014.

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.

A web-based protein interaction network visualizer

BackgroundInteraction between proteins is one of the most important mechanisms in the execution of cellular functions. The study of these interactions has provided insight into the functioning of an organism’s processes. As of October 2013, Homo sapiens had over 170000 Protein-Protein interactions (PPI) registered in the Interologous Interaction Database, which is only one of the many public resources where protein interactions can be accessed. These numbers exemplify the volume of data that research on the topic has generated. Visualization of large data sets is a well known strategy to make sense of information, and protein interaction data is no exception. There are several tools that allow the exploration of this data, providing different methods to visualize protein network interactions. However, there is still no native web tool that allows this data to be explored interactively online.ResultsGiven the advances that web technologies have made recently it is time to bring these interactive views to the web to provide an easily accessible forum to visualize PPI. We have created a Web-based Protein Interaction Network Visualizer: PINV, an open source, native web application that facilitates the visualization of protein interactions (http://biosual.cbio.uct.ac.za/pinv.html). We developed PINV as a set of components that follow the protocol defined in BioJS and use the D3 library to create the graphic layouts. We demonstrate the use of PINV with multi-organism interaction networks for a predicted target from Mycobacterium tuberculosis, its interacting partners and its orthologs.ConclusionsThe resultant tool provides an attractive view of complex, fully interactive networks with components that allow the querying, filtering and manipulation of the visible subset. Moreover, as a web resource, PINV simplifies sharing and publishing, activities which are vital in today’s research collaborative environments. The source code is freely available for download at https://github.com/4ndr01d3/biosual.

Dasty3, a WEB framework for DAS

Motivation: Dasty3 is a highly interactive and extensible Web-based framework. It provides a rich Application Programming Interface upon which it is possible to develop specialized clients capable of retrieving information from DAS sources as well as from data providers not using the DAS protocol. Dasty3 provides significant improvements on previous Web-based frameworks and is implemented using the 1.6 DAS specification. Availability: Dasty3 is an open-source tool freely available at http://www.ebi.ac.uk/dasty/ under the terms of the GNU General public license. Source and documentation can be found at http://code.google.com/p/dasty/. Contact: hhe@ebi.ac.uk

EBI Metagenomics in 2017: Enriching the analysis of microbial communities, from sequence reads to assemblies

Abstract EBI metagenomics (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the analysis and archiving of sequence data derived from the microbial populations found in a particular environment. Over the past two years, EBI metagenomics has increased the number of datasets analysed 10-fold. In addition to increased throughput, the underlying analysis pipeline has been overhauled to include both new or updated tools and reference databases. Of particular note is a new workflow for taxonomic assignments that has been extended to include assignments based on both the large and small subunit RNA marker genes and to encompass all cellular micro-organisms. We also describe the addition of metagenomic assembly as a new analysis service. Our pilot studies have produced over 2400 assemblies from datasets in the public domain. From these assemblies, we have produced a searchable, non-redundant protein database of over 50 million sequences. To provide improved access to the data stored within the resource, we have developed a programmatic interface that provides access to the analysis results and associated sample metadata. Finally, we have integrated the results of a series of statistical analyses that provide estimations of diversity and sample comparisons.

Platelet proteome reveals novel pathways of platelet activation and platelet-mediated immunoregulation in dengue

Dengue is the most prevalent human arbovirus disease worldwide. Dengue virus (DENV) infection causes syndromes varying from self-limiting febrile illness to severe dengue. Although dengue pathophysiology is not completely understood, it is widely accepted that increased inflammation plays important roles in dengue pathogenesis. Platelets are blood cells classically known as effectors of hemostasis which have been increasingly recognized to have major immune and inflammatory activities. Nevertheless, the phenotype and effector functions of platelets in dengue pathogenesis are not completely understood. Here we used quantitative proteomics to investigate the protein content of platelets in clinical samples from patients with dengue compared to platelets from healthy donors. Our assays revealed a set of 252 differentially abundant proteins. In silico analyses associated these proteins with key molecular events including platelet activation and inflammatory responses, and with events not previously attributed to platelets during dengue infection including antigen processing and presentation, proteasome activity, and expression of histones. From these results, we conducted functional assays using samples from a larger cohort of patients and demonstrated evidence for platelet activation indicated by P-selectin (CD62P) translocation and secretion of granule-stored chemokines by platelets. In addition, we found evidence that DENV infection triggers HLA class I synthesis and surface expression by a mechanism depending on functional proteasome activity. Furthermore, we demonstrate that cell-free histone H2A released during dengue infection binds to platelets, increasing platelet activation. These findings are consistent with functional importance of HLA class I, proteasome subunits, and histones that we found exclusively in proteome analysis of platelets in samples from dengue patients. Our study provides the first in-depth characterization of the platelet proteome in dengue, and sheds light on new mechanisms of platelet activation and platelet-mediated immune and inflammatory responses.

iAnn: an event sharing platform for the life sciences

Summary: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available. Availability: http://iann.pro/iannviewer Contact: manuel.corpas@tgac.ac.uk

myKaryoView: a light-weight client for visualization of genomic data

The Distributed Annotation System (DAS) is a protocol for easy sharing and integration of biological annotations. In order to visualize feature annotations in a genomic context a client is required. Here we present myKaryoView, a simple light-weight DAS tool for visualization of genomic annotation. myKaryoView has been specifically configured to help analyse data derived from personal genomics, although it can also be used as a generic genome browser visualization. Several well-known data sources are provided to facilitate comparison of known genes and normal variation regions. The navigation experience is enhanced by simultaneous rendering of different levels of detail across chromosomes. A simple interface is provided to allow searches for any SNP, gene or chromosomal region. User-defined DAS data sources may also be added when querying the system. We demonstrate myKaryoView capabilities for adding user-defined sources with a set of genetic profiles of family-related individuals downloaded directly from 23andMe. myKaryoView is a web tool for visualization of genomic data specifically designed for direct-to-consumer genomic data that uses publicly available data distributed throughout the Internet. It does not require data to be held locally and it is capable of rendering any feature as long as it conforms to DAS specifications. Configuration and addition of sources to myKaryoView can be done through the interface. Here we show a proof of principle of myKaryoViews ability to display personal genomics data with 23andMe genome data sources. The tool is available at: http://mykaryoview.com.