HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions

Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).
Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.
Conclusions: HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes

Abmash: Mashing Up Legacy Web Applications by Automated Imitation of Human Actions

Many business web-based applications do not offer applications programming interfaces (APIs) to enable other applications to access their data and functions in a programmatic manner. This makes their composition difficult (for instance to synchronize data between two applications). To address this challenge, this paper presents Abmash, an approach to facilitate the integration of such legacy web applications by automatically imitating human interactions with them. By automatically interacting with the graphical user interface (GUI) of web applications, the system supports all forms of integrations including bi-directional interactions and is able to interact with AJAX-based applications. Furthermore, the integration programs are easy to write since they deal with end-user, visual user-interface elements. The integration code is simple enough to be called a "mashup".Comment: Software: Practice and Experience (2013)

Towards Social Information Seeking and Interaction on the Web

User generated content is one of the key concepts of the social web (a. k. a “Web 2.0”) and enables users to search and interact with information that has been created (e.g. blogs) or annotated by other users (e.g. in tagging systems). Consequently, information seeking and interaction have been extended by a social dimension. The interaction can be social in so far that user generated content is searched and retrieved or, in a more direct manner that social interactions are carried out before, during or after search by communicating through Web 2.0 features like (micro-)blog posts, comments, and ratings. This paper focuses on social interactions during the search process by combining a model introduced by Shneiderman (2002) which attempts to describe human motivation for collaboratively using computers with an explorative model for social search by Evans and Chi (2008)

Getting grip on complex water issues? : a case study: Rotterdam Mainport, Appropriate Assessment Wadden Sea

In Dutch water systems many human interventions are carried out. These interventions are designed to achieve management goals, like increase protection against flooding, improve environmental quality and/or stimulate the national economy. Decision-makers involved in these kinds of plans have to deal with ecological effects, physical effects, economic costs and benefits and technical feasibility. Furthermore, they operate within a complex web of interactions between policy, regulations, and social and political processes. This PhD-project aims at assisting decision-makers in constructing assessments of the impact of future human interventions in water systems

Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks

In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.
Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from “seed” lists of human Entrez gene names. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is available at http://actin.pharm.mssm.edu/genes2networks.
Genes2Network is a powerful web-based software application tool that can help experimental biologists to interpret high-throughput experimental results used in genomics and proteomics studies where the output of these experiments is a list of significantly changing genes or proteins. The system can be used to find relationships between nodes from the seed list, and predict novel nodes that play a key role in a common function

A Storm in an IoT Cup: The Emergence of Cyber-Physical Social Machines

The concept of social machines is increasingly being used to characterise various socio-cognitive spaces on the Web. Social machines are human collectives using networked digital technology which initiate real-world processes and activities including human communication, interactions and knowledge creation. As such, they continuously emerge and fade on the Web. The relationship between humans and machines is made more complex by the adoption of Internet of Things (IoT) sensors and devices. The scale, automation, continuous sensing, and actuation capabilities of these devices add an extra dimension to the relationship between humans and machines making it difficult to understand their evolution at either the systemic or the conceptual level. This article describes these new socio-technical systems, which we term Cyber-Physical Social Machines, through different exemplars, and considers the associated challenges of security and privacy.Comment: 14 pages, 4 figure

The Interactive Minority Game: a Web based investigation of human market interactions

The unprecedented access offered by the World Wide Web brings with it the potential to gather huge amounts of data on human activities. Here we exploit this by using a toy model of financial markets, the Minority Game (MG), to investigate human speculative trading behaviour and information capacity. Hundreds of individuals have played a total of tens of thousands of game turns against computer-controlled agents in the Web-based Interactive Minority Game. The analytical understanding of the MG permits fine-tuning of the market situations encountered, allowing for investigation of human behaviour in a variety of controlled environments. In particular, our results indicate a transition in players' decision-making, as the markets become more difficult, between deductive behaviour making use of short-term trends in the market, and highly repetitive behaviour that ignores entirely the market history, yet outperforms random decision-making.Experimental economics and financial markets; Decision theory and game theory; Information theory

Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks

In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.
Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from “seed” lists of human Entrez gene names. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is available at http://actin.pharm.mssm.edu/genes2networks.
Genes2Network is a powerful web-based software application tool that can help experimental biologists to interpret high-throughput experimental results used in genomics and proteomics studies where the output of these experiments is a list of significantly changing genes or proteins. The system can be used to find relationships between nodes from the seed list, and predict novel nodes that play a key role in a common function

Towards Multi-Modal Interactions in Virtual Environments: A Case Study

We present research on visualization and interaction in a realistic model of an existing theatre. This existing ‘Muziek¬centrum’ offers its visitors information about performances by means of a yearly brochure. In addition, it is possible to get information at an information desk in the theatre (during office hours), to get information by phone (by talking to a human or by using IVR). The database of the theater holds the information that is available at the beginning of the ‘theatre season’. Our aim is to make this information more accessible by using multi-modal accessible multi-media web pages. A more general aim is to do research in the area of web-based services, in particu¬lar interactions in virtual environments

Characterizing web pornography consumption from passive measurements

Web pornography represents a large fraction of the Internet traffic, with thousands of websites and millions of users. Studying web pornography consumption allows understanding human behaviors and it is crucial for medical and psychological research. However, given the lack of public data, these works typically build on surveys, limited by different factors, e.g. unreliable answers that volunteers may (involuntarily) provide. In this work, we collect anonymized accesses to pornography websites using HTTP-level passive traces. Our dataset includes about $15\,000$ broadband subscribers over a period of 3 years. We use it to provide quantitative information about the interactions of users with pornographic websites, focusing on time and frequency of use, habits, and trends. We distribute our anonymized dataset to the community to ease reproducibility and allow further studies.Comment: Passive and Active Measurements Conference 2019 (PAM 2019). 14 pages, 7 figure