In Silico Characterization of Proteins: UniProt,InterPro and Integr8

Nucleic acid sequences from genome sequencing projects are submitted as raw data, from which biologists attempt to elucidate the function of the predicted gene products. The protein sequences are stored in public databases, such as the UniProt Knowledgebase (UniProtKB), where curators try to add predicted and experimental functional information. Protein function prediction can be done using sequence similarity searches, but an alternative approach is to use protein signatures, which classify proteins into families and domains. The major protein signature databases are available through the integrated InterPro database, which provides a classification of UniProtKB sequences. As well as characterization of proteins through protein families, many researchers are interested in analyzing the complete set of proteins from a genome (i.e. the proteome), and there are databases and resources that provide non-redundant proteome sets and analyses of proteins from organisms with completely sequenced genomes. This article reviews the tools and resources available on the web for single and large-scale protein characterization and whole proteome analysis.     

Genomics made easier: An introductory tutorial to genome datamining

Integrated genome databases – such as the UCSC, Ensembl and NCBI MapViewer databases – and their associated data querying and visualization interfaces (e.g. the genome browsers) have transformed the way that molecular biologists, geneticists and bioinformaticists analyze genomic data. Nevertheless, because of the complexity of these tools, many researchers take advantage of only a fraction of their capabilities. In this tutorial, using examples from medical genetics and alternative splicing, I describe some of the biological questions that can be addressed with these techniques. I also show why doing so typically is more effective than using alternative methods and indicate some of the resources available for learning more about the advanced capabilities of these powerful tools.     

The NIDDK Information Network: A Community Portal for Finding Data,Materials, and Tools for Researchers Studying Diabetes,Digestive, and Kidney Diseases

The NIDDK Information Network (dkNET; http://dknet.org) was launched to serve the needs of basic and clinical investigators in metabolic, digestive and kidney disease by facilitating access to research resources that advance the mission of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). By research resources, we mean the multitude of data, software tools, materials, services, projects and organizations available to researchers in the public domain. Most of these are accessed via web-accessible databases or web portals, each developed, designed and maintained by numerous different projects, organizations and individuals. While many of the large government funded databases, maintained by agencies such as European Bioinformatics Institute and the National Center for Biotechnology Information, are well known to researchers, many more that have been developed by and for the biomedical research community are unknown or underutilized. At least part of the problem is the nature of dynamic databases, which are considered part of the “hidden” web, that is, content that is not easily accessed by search engines. dkNET was created specifically to address the challenge of connecting researchers to research resources via these types of community databases and web portals. dkNET functions as a “search engine for data”, searching across millions of database records contained in hundreds of biomedical databases developed and maintained by independent projects around the world. A primary focus of dkNET are centers and projects specifically created to provide high quality data and resources to NIDDK researchers. Through the novel data ingest process used in dkNET, additional data sources can easily be incorporated, allowing it to scale with the growth of digital data and the needs of the dkNET community. Here, we provide an overview of the dkNET portal and its functions. We show how dkNET can be used to address a variety of use cases that involve searching for research resources.     

Web Tools for Rice Transcriptome Analyses

Gene expression databases provide profiling data for the expression of thousands of genes to researchers worldwide. Oligonucleotide microarray technology is a useful tool that has been employed to produce gene expression profiles in most species. In rice, there are five genome-wide DNA microarray platforms: NSF 45K, BGI/Yale 60K, Affymetrix, Agilent Rice 44K, and NimbleGen 390K. Presently, more than 1,700 hybridizations of microarray gene expression data are available from public microarray depositing databases such as NCBI gene expression omnibus and Arrayexpress at EBI. More processing or reformatting of public gene expression data is required for further applications or analyses. Web-based databases for expression meta-analyses are useful for guiding researchers in designing relevant research schemes. In this review, we summarize various databases for expression meta-analyses of rice genes and web tools for further applications, such as the development of co-expression network or functional gene network.     

Jemboss reloaded

Bioinformatics tools are freely available from websites all over the world. Often they are presented as web services, although there are many tools for download and use on a local machine. This tutorial section looks at Jemboss, a Java-based graphical user interface (GUI) for the EMBOSS bioinformatics suite, which combines the advantages of both web service and downloaded software.     

Methods for facilitating web-based participatory research informatics

Scientific datasets are often generated and used by “communities”, or groups of users and creators. These communities, today often virtual, can include researchers, decision-makers, and the general public; participants in these communities may contribute different components during various iterations in the data generation process, and have different needs for resulting data products. As this “participatory research informatics” model, which includes elements of collaborative research, public participation, and digital data libraries, becomes the norm, new approaches to dynamic data management will be important. Researchers commonly use the web as a medium for research collaboration among colleagues, as well as to disseminate results to decision-makers and the public. In addition, the web can be used to facilitate dynamic collaboration by allowing research-in-progress to be accessed and edited by multiple participants. Indeed, one key benefit of using the web to facilitate research projects is that data can undergo revisions and corrections while being displayed in some form over the web. However, it can be a challenge to keep track of multiple edits to files while maintaining the integrity of a web-interface. Here we describe a system for promoting collaboration in the creation, maintenance, and use of dynamic data over the web. Using simple Microsoft Excel spreadsheets combined with traditional relational databases to facilitate dynamic data generation and updates and maintain a data schema, we are able to facilitate efficient collaboration within and among participant communities. This approach allows for the separation of web display and content, which in turn allows participants to be responsible for their own content. This separation simplifies the interaction between those responsible for the content (researchers and other participants), those responsible for the data display (web designers), and those responsible for data management, storage, and retrieval (web programmers). The approach described here is particularly well suited to large, spatially-specific ecological datasets because it can be used to facilitate the “real-time” editing and display of visual data such as web-maps, as well as to encourage multiple participants to both contribute to and interact with “beta” data and content.     

PGV - Prokaryotic Genome Viewer

Recent sequencing of genomes of several microorganisms provides an opportunity to have access to huge volumes of data stored in various databases. This has resulted in the development of various computational and visualization tools to aid in retrieval and analysis of data. Development of user friendly genome data mapping and visualization tools facilitates researchers to closely examine various features of genes and make inferences from the displayed data efficiently. PGV - Prokaryotic Genome Viewer is a Java based web application tool capable of generating high quality interactive circular chromosome maps. With simple mouse roll over tasks on the interested region on the displayed map, the user is provided with features such as feature labeling, multi-fold zooming, image rotation and hyperlinking to different information resources. The tool is capable of instantaneously generating maps using user-supplied sequence data.     

Facial attractiveness ratings from video-clips and static images tell the same story

Most of what we know about what makes a face attractive and why we have the preferences we do is based on attractiveness ratings of static images of faces, usually photographs. However, several reports that such ratings fail to correlate significantly with ratings made to dynamic video clips, which provide richer samples of appearance, challenge the validity of this literature. Here, we tested the validity of attractiveness ratings made to static images, using a substantial sample of male faces. We found that these ratings agreed very strongly with ratings made to videos of these men, despite the presence of much more information in the videos (multiple views, neutral and smiling expressions and speech-related movements). Not surprisingly, given this high agreement, the components of video-attractiveness were also very similar to those reported previously for static-attractiveness. Specifically, averageness, symmetry and masculinity were all significant components of attractiveness rated from videos. Finally, regression analyses yielded very similar effects of attractiveness on success in obtaining sexual partners, whether attractiveness was rated from videos or static images. These results validate the widespread use of attractiveness ratings made to static images in evolutionary and social psychological research. We speculate that this validity may stem from our tendency to make rapid and robust judgements of attractiveness.     

Using computer-based tutorials to encourage reflection

There is some evidence to suggest that undergraduate biology students need to be given more opportunities for reflection in their education. Some argue that computer-based learning packages may be able to offer such opportunities. This paper presents four different approaches to defining what reflection is and how it can be promoted. These approaches are then used to discuss and review the different ways in which computer-based tutorials can be used to promote lateral thinking. An example of a web-based biology tutorial called ‘How Now Mad Cow’ is described and preliminary evaluation results are presented, in order to illustrate how students may be encouraged to reflect and what factors may influence that. Finally, the role of the tutor in enspiring students to reflect while using computer-based tutorials is discussed. This distinguishes between the role of the tutor in designing a computer-based tutorial, and the role of the tutor in determining and facilitating how a student uses a tutorial once it has been designed.     

High performance web server architecture with Kernel-level caching

In this work we are focusing on reducing response time and bandwidth requirements for high performance web server. Many researches have been done in order to improve web server performance by modifying the web server architecture. In contrast to these approaches, we take a different point of view, in which we consider the web server performance in OS perspective rather than web server architecture itself. To achieve these purposes we are exploring two different approaches. The first is running web server within OS kernel. We use kHTTPd as our basis for implementation. But it has a several drawbacks such as copying data redundantly, synchronous write, and processing only static data. We propose some techniques to improve these flaws. The second approach is caching dynamic data. Dynamic data can seriously reduce the performance of web servers. Caching dynamic data has been thought difficult to cache because it often change a lot more frequently than static pages and because web server needs to access database to provide service with dynamic data. To this end, we propose a solution for higher performance web service by caching dynamic data using content separation between static and dynamic portions. Benchmark results using WebStone show that our architecture can improve server performance by up to 18 percent and can reduce user’s perceived latency significantly.     

Behavioral responses of silverback gorillas (Gorilla gorilla gorilla) to videos

This study examined the impact of video presentations on the behavior of 4 silverback, western lowland gorillas (Gorilla gorilla gorilla). On each of 5 occasions, gorillas viewed 6 types of videos (blue screen, humans, an all-male or mixed-sex group engaged in low activity, and an all-male or mixed-sex group engaged in agonistic behavior). The study recorded behavioral responses and watching rates. All gorillas preferred dynamic over static videos; 3 watched videos depicting gorillas significantly more than those depicting humans. Among the gorilla videos, the gorillas clearly preferred watching the mixed-sex group engaged in agonistic behavior; yet, this did not lead to an increase in aggression or behavior indicating agitation. Further, habituation to videos depicting gorillas did not occur. This supports the effectiveness of this form of enrichment, particularly for a nonhuman animal needing to be separated temporarily due to illness, shipment quarantine, social restructuring, or exhibit modification.     

Behavioral Responses of Silverback Gorillas (Gorilla gorilla gorilla) to Videos

This study examined the impact of video presentations on the behavior of 4 silverback, western lowland gorillas (Gorilla gorilla gorilla). On each of 5 occasions, gorillas viewed 6 types of videos (blue screen, humans, an all-male or mixed-sex group engaged in low activity, and an all-male or mixed-sex group engaged in agonistic behavior). The study recorded behavioral responses and watching rates. All gorillas preferred dynamic over static videos; 3 watched videos depicting gorillas significantly more than those depicting humans. Among the gorilla videos, the gorillas clearly preferred watching the mixed-sex group engaged in agonistic behavior; yet, this did not lead to an increase in aggression or behavior indicating agitation. Further, habituation to videos depicting gorillas did not occur. This supports the effectiveness of this form of enrichment, particularly for a nonhuman animal needing to be separated temporarily due to illness, shipment quarantine, social restructuring, or exhibit modification.     

TVNViewer: an interactive visualization tool for exploring networks that change over time or space

The relationship between genes and proteins is a dynamic relationship that changes across time and differs in different cells. The study of these differences can reveal various insights into biological processes and disease progression, especially with the aid of proper tools for network visualization. Toward this purpose, we have developed TVNViewer, a novel visualization tool, which is specifically designed to aid in the exploration and analysis of dynamic networks. AVAILABILITY: TVNViewer is freely available with documentation and tutorials on the web at http://sailing.cs.cmu.edu/tvnviewer. CONTACT: epxing@cs.cmu.edu.     

Beyond ‘Riot Porn’: Protest Video and the Production of Unruly Subjects

From the globalization protests of the previous decade to the more recent Occupy Movement, activists have embraced the use of digital video. Many appropriations of the technology, including those by human rights advocates, rest on the theory that ‘seeing is believing’ and understand video to be uniquely suited to forms of truth telling such as witnessing, documenting and reporting. While I encountered such realist uses of video during fieldwork with direct action movements in the former Yugoslavia, activists are also preoccupied with videos depicting the most physical confrontations with the police, videos they sometimes referred to as ‘riot porn’. They engage these videos for the sensory, affective and bodily experiences they facilitate. Indeed, activist practices around and claims for video indicate that they understand video as a technology of the self, using it to forge emotional relationships with activists elsewhere, steel themselves for physical confrontation and cultivate new political desires.     

Video on the Internet: An introduction to the digital encoding, compression, and transmission of moving image data

In this paper, we seek to provide an introduction to the fast-moving field of digital video on the Internet, from the viewpoint of the biological microscopist who might wish to store or access videos, for instance in image databases such as the BioImage Database (http://www.bioimage.org). We describe and evaluate the principal methods used for encoding and compressing moving image data for digital storage and transmission over the Internet, which involve compromises between compression efficiency and retention of image fidelity, and describe the existing alternate software technologies for downloading or streaming compressed digitized videos using a Web browser. We report the results of experiments on video microscopy recordings and three-dimensional confocal animations of biological specimens to evaluate the compression efficiencies of the principal video compression-decompression algorithms (codecs) and to document the artefacts associated with each of them. Because MPEG-1 gives very high compression while yet retaining reasonable image quality, these studies lead us to recommend that video databases should store both a high-resolution original version of each video, ideally either uncompressed or losslessly compressed, and a separate edited and highly compressed MPEG-1 preview version that can be rapidly downloaded for interactive viewing by the database user.     

Wild birds in YouTube videos: Presence of specific species contributes to increased views

Recent advances in understanding cultural ecosystem services (CES) using big data such as social media and other web archives have been primarily made to identify the relationships between the specific indicators for CES and large-scale features of ecosystems, such as vegetation covers and types, ecosystem types, naturalness, and the proportion of areas designated as protected areas. Yet, we know little about how biodiversity and specific species contribute to the enhancement of CES. Here, we examined the factors influencing the number of views in YouTube videos displaying wild birds in nature as a direct indicator of CES related to aesthetic enjoyment, environmental education, and nature experience. We found that the presence of specific wild bird species (i.e., Streptopelia orientalis and Larvivora cyane) increased the number of views while controlling for confounding factors such as the length of the video and the number of days since uploading. We suggest that these species are widely recognized, positively perceived presumably owing to their cultural significance, and preferred among viewers watching videos of wild birds, resulting in more views for videos including these species. Finally, we depicted the geographic distribution (on a national scale) of YouTube videos displaying wild birds in nature. Urban and agricultural land cover around the geotagged location of each video negatively affected the number of views, suggesting that over-exploitation of ecosystems may lead to the loss of important CES. Our study thus demonstrates the contributions of specific wild bird species to enhancing the CES related to aesthetic enjoyment, environmental education, and nature experience, provided through online shared videos.     

How to build and install your own CaptuRING

CaptuRING is a reliable and affordable tool to transform tree-ring samples into digital images combining open source software and do-it-yourself philosophies. A Raspberry Pi runs the system through an Arduino board that controls the wood sample movement across a linear screw at the time that a digital camera takes sequential high resolution (>4500 dpi) images from a wood sample. Here, we present three video tutorials, with English and Spanish subtitles, to construct and install CaptuRING (github.com/CambiumRG/CaptuRING) from scratch. First video tutorial explains the necessary components and how to assemble them to construct the CaptuRING platform, second tutorial covers Arduino board and Raspberry Pi connections, and the third tutorial is devoted to hardware configuration, software installation and CaptuRING use.     

Workflow management systems for gene sequence analysis and evolutionary studies – A Review

Post ‘omic’ era has resulted in the development of many primary, secondary and derived databases. Many analytical and visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.