Available online at http://nashua.case.edu/pathways

Supplementary data are available at Bioinformatics online.

With the recent advances in experimental technologies, such as gas chromatography and mass spectrometry, the number of metabolites that can be measured in biofluids of individuals has markedly increased. Given a set of such measurements, a very common task encountered by biologists is to identify the metabolic mechanisms that lead to changes in the concentrations of given metabolites and interpret the metabolic consequences of the observed changes in terms of physiological problems, nutritional deficiencies, or diseases. In this paper, we present the steady-state metabolic network dynamics analysis (SMDA) approach in detail, together with its application in a cystic fibrosis study. We also present a computational performance evaluation of the SMDA tool against a mammalian metabolic network database. The query output space of the SMDA tool is exponentially large in the number of reactions of the network. However, (i) larger numbers of observations exponentially reduce the output size, and (ii) exploratory search and browsing of the query output space is provided to allow users to search for what they are looking for.

Predicting promising academic papers is useful for a variety of parties, including researchers, universities, scientific councils, and policymakers. Researchers may benefit from such data to narrow down their reading list and focus on what will be important, and policymakers may use predictions to infer rising fields for a more strategic distribution of resources. This paper proposes a novel technique to predict a paper's future impact (i.e., number of citations) by using temporal and topological features derived from citation networks. We use a behavioral modeling approach in which the temporal change in the number of citations a paper gets is clustered, and new papers are evaluated accordingly. Then, within each cluster, we model the impact prediction as a regression problem where the objective is to predict the number of citations that a paper will get in the near or far future, given the early citation performance of the paper. The results of empirical evaluations on data from several well-known citation databases show that the proposed framework performs significantly better than the state of the art approaches.

BackgroundIntegration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks.DescriptionPathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database.ConclusionsPathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world.