Integration and visualisation of data in bioinformatics

Includes bibliographical referencesThe most recent advances in laboratory techniques aimed at observing and measuring biological processes are characterised by their ability to generate large amounts of data. The more data we gather, the greater the chance of finding clues to understand the systems of life. This, however, is only true if the methods that analyse the generated data are efficient, effective, and robust enough to overcome the challenges intrinsic to the management of big data. The computational tools designed to overcome these challenges should also take into account the requirements of current research. Science demands specialised knowledge for understanding the particularities of each study; in addition, it is seldom possible to describe a single observation without considering its relationship with other processes, entities or systems. This thesis explores two closely related fields: the integration and visualisation of biological data. We believe that these two branches of study are fundamental in the creation of scientific software tools that respond to the ever increasing needs of researchers. The distributed annotation system (DAS) is a community project that supports the integration of data from federated sources and its visualisation on web and stand-alone clients. We have extended the DAS protocol to improve its search capabilities and also to support feature annotation by the community. We have also collaborated on the implementation of MyDAS, a server to facilitate the publication of biological data following the DAS protocol, and contributed in the design of the protein DAS client called DASty. Furthermore, we have developed a tool called probeSearcher, which uses the DAS technology to facilitate the identification of microarray chips that include probes for regions on proteins of interest. Another community project in which we participated is BioJS, an open source library of visualisation components for biological data. This thesis includes a description of the project, our contributions to it and some developed components that are part of it. Finally, and most importantly, we combined several BioJS components over a modular architecture to create PINV, a web based visualiser of protein-protein interaction (PPI) networks, that takes advantage of the features of modern web technologies in order to explore PPI datasets on an almost ubiquitous platform (the web) and facilitates collaboration between scientific peers. This thesis includes a description of the design and development processes of PINV, as well as current use cases that have benefited from the tool and whose feedback has been the source of several improvements to PINV. Collectively, this thesis describes novel software tools that, by using modern web technologies, facilitates the integration, exploration and visualisation of biological data, which has the potential to contribute to our understanding of the systems of life

DAS Writeback: A Collaborative Annotation System for Proteins

We designed and developed a Collaborative Annotation System for Proteins called DAS Writeback, which extends the Distributed Annotation System (DAS) to provide the functionalities of adding, editing and deleting annotations. A great deal of effort has gone into gathering information about proteins over the last few years. By June 2009, UniProtKB/Swiss-Prot, a curated database, contained over four hundred thousand sequence entries and UniProtKB/TrEMBL, a database with automated annotation, contained over eight million sequence entries. Every protein is annotated with relevant information, which needs to be eciently captured and made available to other research groups. These include annotations about the structure, the function or the biochemical residues. Several research groups have taken on the task of making this information accessible to the community, however, information flow in the opposite direction has not been extensively explored. Users are currently passive actors that behave as consumers of one or several sources of protein annotations and they have no immediate way to provide feedback to the source if, for example, a mistake is detected or they want to add information. Any change has to be done by the owner of the database. The current lack of being able to feed information back to a database is tackled in this project. The solution consists of an extension of the DAS protocol that defines the communication rules between the client and the writeback server following the Uniform Interface of the RESTful architecture. A protocol extension was proposed to the DAS community and implementations of both server and client were created in order to have a fully functional system. For the development of the server, writing functionalities were added to MyDAS, which is a widely used DAS server. The writeback client is an extended version of the web-based protein client Dasty2. The involvement of the DAS community and other potential users was a fundamental component of this project. The architecture was designed with the insight of the DAS specialized forum, a prototype was then created and subsequently presented in the DAS workshop 2009. The feedback from the forum and workshop was used to redefine the architecture and implement the system. A usability experiment was performed using potential users of the system emulating a real annotation task. It demonstrated that DAS writeback is effective, usable and will provide the appropriate environment for the creation and evolution of a protein annotation community. Although the scope of this research is limited to protein annotations, the specification was defined in a general way. It can, therefore, be used for other types of information supported by DAS, implying that the server is versatile enough to be used in other scenarios without major modifications

Ultrasound potentialities on the determination of the pesticide carbaryl using diamond electrodes

The potentiality of the use of ultrasound radiation in association with a boron-doped diamond electrode was evaluated on the voltammetric determination of the pesticide carbaryl. Improvements in the sensitivity, limit of detection and reproducibility of the measurements were observed due to both, the enhancement of mass transport and the cleaning of the electrode surface provided by ultrasound. Satisfactory recovery levels for carbaryl in pure water (96-98%) and pineapple juice (89-92%) for quiescent and sonovoltammetric methodologies were obtained. These methodologies can be alternative tools for the analyses of pesticides in fruit samples, mainly the insonated condition that improve the analytical performance and dispense intermediary cleanings of the electrode surface.CNPqFapes

Residuos agroindustriales como fuente de nutrientes y compuestos fenólicos

El presente trabajo describe los nutrientes y compuestos fenólicos contenidos en diversos residuos agroindustriales (RAI). Los RAI pueden derivar en problemas que comprometen la alimentación y salud de las poblaciones más vulnerables si no son aprovechados adecuadamente. Por ello  es importante crear alternativas que contribuyan a contrarrestar el problema, desde la producción de alimentos hasta la mesa del consumidor. Los RAI de frutas, verduras, cereales y oleaginosas contienen nutrientes y compuestos fenólicos que pueden ser benéficos a la salud debido a sus efectos antioxidantes, antiinflamatorios, antidiabéticos, entre otros. Los RAI podrían también ser aplicados en el desarrollo de alimentos, debido a sus características tecnofuncionales como la capacidad de actuar como agentes gelificantes, emulsificantes, estabilizantes y espesantes. De acuerdo con lo anterior, el empleo de RAI para un segundo uso es prometedor, sin embargo, aún quedan algunos retos por resolver, tales como el escalamiento y la optimización de su extracción

MyDas, an extensible Java DAS server

A large number of diverse, complex, and distributed data resources are currently available in the Bioinformatics domain. The pace of discovery and the diversity of information means that centralised reference databases like UniProt and Ensembl cannot integrate all potentially relevant information sources. From a user perspective however, centralised access to all relevant information concerning a specific query is essential. The Distributed Annotation System (DAS) defines a communication protocol to exchange annotations on genomic and protein sequences; this standardisation enables clients to retrieve data from a myriad of sources, thus offering centralised access to end-users. We introduce MyDas, a web server that facilitates the publishing of biological annotations according to the DAS specification. It deals with the common functionality requirements of making data available, while also providing an extension mechanism in order to implement the specifics of data store interaction. MyDas allows the user to define where the required information is located along with its structure, and is then responsible for the communication protocol details

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

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: Mock galaxy catalogues for the BOSS Final Data Release

We reproduce the galaxy clustering catalogue from the SDSS-III Baryon Oscillation Spectroscopic Survey Final Data Release (BOSS DR11 and DR12) with high fidelity on all relevant scales in order to allow a robust analysis of baryon acoustic oscillations and redshift space distortions. We have generated (6000) 12 288 MultiDark PATCHY BOSS (DR11) DR12 light cones corresponding to an effective volume of ~ 192 000 [h-1 Gpc]3 (the largest ever simulated volume), including cosmic evolution in the redshift range from 0.15 to 0.75. The mocks have been calibrated using a reference galaxy catalogue based on the halo abundance matching modelling of the BOSS DR11 and DR12 galaxy clustering data and on the data themselves. The production follows three steps. First, we apply the PATCHY code to generate a dark matter field and an object distribution including non-linear stochastic galaxy bias. Secondly, we run the halo/stellar distribution reconstruction HADRON code to assign masses to the various objects. This step uses the mass distribution as a function of local density and non-local indicators (i.e. tidal field tensor eigenvalues and relative halo exclusion separation for massive objects) from the reference simulation applied to the corresponding patchy dark matter and galaxy distribution. Finally, we apply the SUGAR code to build the light cones. The resulting MultiDarkPATCHY mock light cones reproduce the number density, selection function, survey geometry, and in general within 1s, for arbitrary stellar mass bins, the power spectrum up to k = 0.3 h Mpc-1, the two-point correlation functions down to a few Mpc scales, and the three-point statistics of the BOSS DR11 and DR12 galaxy samples.Fil: Kitaura, Francisco-Shu. Leibniz-Institut für Astrophysik Potsdam; AlemaniaFil: Rodriguez Torres, Sergio A.. Universidad Autónoma de Madrid; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Chuang, Chia Hsun. Universidad Autónoma de Madrid; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Zhao, Cheng. Tsinghua University; ChinaFil: Prada, Francisco. Consejo Superior de Investigaciones Científicas; España. Universidad Autónoma de Madrid; EspañaFil: Gil Marín, Héctor. University of Portsmouth; Reino UnidoFil: Guo, Hong. State University of Utah; Estados Unidos. Shanghai Astronomical Observatory; ChinaFil: Yepes, Gustavo. Universidad Autónoma de Madrid. Facultad de Ciencias; EspañaFil: Klypin, Anatoly. Universidad Autónoma de Madrid; España. Consejo Superior de Investigaciones Científicas; España. New Mexico State University; Estados UnidosFil: Scoccola, Claudia Graciela. Universidad Autónoma de Madrid; España. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; Argentina. Instituto de Astrof{isica de Canarias; España. Universidad de La Laguna; EspañaFil: Tinker, Jeremy. University of New York; Estados UnidosFil: McBride, Cameron. Harvard-Smithsonian Center for Astrophysics; Estados UnidosFil: Reid, Beth. Lawrence Berkeley National Laboratory; Estados Unidos. University of California at Berkeley; Estados UnidosFil: Sánchez, Ariel G.. Max Planck Institut für Extraterrestrische Physik; AlemaniaFil: Salazar Albornoz, Salvador. Max Planck Institut für Extraterrestrische Physik; Alemania. Ludwig Maximilians Universitat; AlemaniaFil: Grieb, Jan Niklas. Max Planck Institut für Extraterrestrische Physik; Alemania. Ludwig Maximilians Universitat; AlemaniaFil: Vargas Magana, Mariana. Universidad Nacional Autónoma de México; MéxicoFil: Cuesta, Antonio J.. Universidad de Barcelona; EspañaFil: Neyrinck, Mark. University Johns Hopkins; Estados UnidosFil: Beutler, Florian. Lawrence Berkeley National Laboratory; Estados UnidosFil: Comparat, Johan. Universidad Autónoma de Madrid; España. Consejo Superior de Investigaciones Científicas; EspañaFil: Percival, Will J.. University of Portsmouth; Reino UnidoFil: Ross, Ashley. Ohio State University; Estados Unidos. University of Portsmouth; Reino Unid

The Extrusion Process as an Alternative for Improving the Biological Potential of Sorghum Bran: Phenolic Compounds and Antiradical and Anti-Inflammatory Capacity

Approximately 80% of sorghum phenolic compounds are linked to arabinoxylans by ester bonds, which are capable of resisting the digestion process in the upper gastrointestinal tract, compromising their bioaccessibility and biological potential. The aim of this study was to evaluate the effect of the extrusion process on the content of phenolic compounds in sorghum bran and its impact on phenolic compounds and antiradical and anti-inflammatory capacity. Results revealed that the extrusion process increased total phenol content in sorghum bran compared to nonextruded sorghum, particularly for extrusion at 180°C with 20% moisture content (2.0222±0.0157 versus 3.0729±0.0187 mg GAE/g +52%), which positively affected antiradical capacity measured by the DPPH and TEAC assays. The percentage of inhibition of nitric oxide (NO) production by RAW cells due to the presence of extruded sorghum bran extract was significantly higher than that of nonextruded sorghum bran extract (90.2±1.9% versus 76.2±1.3%). The results suggest that extruded sorghum bran could be used as a functional ingredient and provide advantages to consumers by reducing diseases related to oxidative stress and inflammation

A web-based protein interaction network visualizer

Abstract Background Interaction 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. Results Given 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. Conclusions The 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

DAS Writeback: A Collaborative Annotation System

<p>Abstract</p> <p>Background</p> <p>Centralised resources such as GenBank and UniProt are perfect examples of the major international efforts that have been made to integrate and share biological information. However, additional data that adds value to these resources needs a simple and rapid route to public access. The Distributed Annotation System (DAS) provides an adequate environment to integrate genomic and proteomic information from multiple sources, making this information accessible to the community. DAS offers a way to distribute and access information but it does not provide domain experts with the mechanisms to participate in the curation process of the available biological entities and their annotations.</p> <p>Results</p> <p>We designed and developed a Collaborative Annotation System for proteins called DAS Writeback. DAS writeback is a protocol extension of DAS to provide the functionalities of adding, editing and deleting annotations. We implemented this new specification as extensions of both a DAS server and a DAS client. The architecture was designed with the involvement of the DAS community and it was improved after performing usability experiments emulating a real annotation task.</p> <p>Conclusions</p> <p>We demonstrate that DAS Writeback is effective, usable and will provide the appropriate environment for the creation and evolution of community protein annotation.</p