{"title":"Exact and Approximate Stochastic Simulations of the MAPK Pathway and Comparisons of Simulations Results","authors":"Vilda Purutçuoglu Gazi, E. Wit","doi":"10.2390/biecoll-jib-2006-38","DOIUrl":"https://doi.org/10.2390/biecoll-jib-2006-38","url":null,"abstract":"The MAPK (mitogen-activated protein kinase) or its synonymous ERK (extracellular signal regulated kinase) pathway whose components are Ras, Raf, and MEK proteins with many biochemical links, is one of the major signalling systems involved in cellular growth control of eukaryotes including cell proliferation, transformation, differentiation, and apoptosis. In this study we describe the MAPK/ERK pathway via (quasi) biochemical reactions and then implement the pathway by a stochastic Markov process. A novelty of our approach is to use multiple parametrizations in order to deal with molecules for which localization in the cell is an intricate part of the dynamic process and to describe the protein using different binding sites and various phosphorylations. We simulate the system by exact and different approximate simulations, e.g. via the Poisson τ -leap, the Binomial τ leap and the diffusion methods, in which we introduce a new updating plan for dependent columns of the diffusion matrix. Finally we compare the results of different algorithms by the current biological knowledge and find out new relations about this complex system.","PeriodicalId":256361,"journal":{"name":"J. Integr. Bioinform.","volume":"82 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134325714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Kaps, K. Dyshlevoi, K. Heumann, R. Jost, Ioannis Kontodinas, Martin Wolff, J. Hani
{"title":"The BioRS(TM) Integration and Retrieval System: An open system for distributed data integration","authors":"A. Kaps, K. Dyshlevoi, K. Heumann, R. Jost, Ioannis Kontodinas, Martin Wolff, J. Hani","doi":"10.2390/biecoll-jib-2006-44","DOIUrl":"https://doi.org/10.2390/biecoll-jib-2006-44","url":null,"abstract":"Modern academic and industrial research in life sciences generates huge amounts of data and information. To extract knowledge from this information space, optimized integration and retrieval software tools are essential. In the last years, a number of academic as well as commercial systems have been developed to solve this problem. However, as scientific projects are distributed at different locations (e.g., subsidiaries of companies, academic partnerships), data exchange and availability must be realized in a way that avoids data replication. In this article, we describe a global solution for integrating distributed information by applying the BioRSTM Integration and Retrieval System and its inter-BioRS communication capability that goes beyond the standard issue of local data integration. Each site integrates and maintains locally generated data using a local copy of the BioRS software. Applying the inter-BioRS communication, all available BioRS instances can communicate with each other realizing a global network of integrated databanks. All databanks integrated in this network can be accessed from any site without any data replication. This open system allows the addition of new information and sites dynamically. However, access privileges for certain databanks can be maintained on a per user and databank level ensuring data security when required.","PeriodicalId":256361,"journal":{"name":"J. Integr. Bioinform.","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124374934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The GeWare data warehouse platform for the analysisof molecular-biological and clinical data","authors":"E. Rahm, T. Kirsten, Jörg Lange","doi":"10.2390/biecoll-jib-2007-47","DOIUrl":"https://doi.org/10.2390/biecoll-jib-2007-47","url":null,"abstract":"We introduce the GeWare data warehouse platform for the integrated analysis of clinical information, microarray data and annotations within large biomedical research studies. Clinical data is obtained from a commercial study management system while publicly available data is integrated using a mediator approach. The platform utilizes a generic approach to manage different types of annotations. We outline the overall architecture of the platform, its implementation as well as the main processing and analysis workflows.","PeriodicalId":256361,"journal":{"name":"J. Integr. Bioinform.","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129482922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. Baumbach, A. Bunkowski, Sita Lange, T. Oberwahrenbrock, Nils Kleinbölting, S. Rahmann, J. Baumbach
{"title":"IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath","authors":"J. Baumbach, A. Bunkowski, Sita Lange, T. Oberwahrenbrock, Nils Kleinbölting, S. Rahmann, J. Baumbach","doi":"10.2390/biecoll-jib-2007-75","DOIUrl":"https://doi.org/10.2390/biecoll-jib-2007-75","url":null,"abstract":"IMS2 is an Integrated Medical Software system for the analysis of Ion Mobility Spectrometry (IMS) data. It assists medical staff with the following IMS data processing steps: acquisition, visualization, classification, and annotation. IMS2 provides data analysis and interpretation features on the one hand, and also helps to improve the classification by increasing the number of the pre-classified datasets on the other hand. It is designed to facilitate early detection of lung cancer, one of the most common cancer types with one million deaths each year around the world. After reviewing the IMS technology, we first describe the software architecture of IMS2 and then the integrated classification module, including necessary pre-processing steps and different classification methods. The Lung Hospital Hemer (Germany) provided IMS data of 35 patients suffering from lung cancer and 72 samples of healthy persons. IMS2 correctly classifies 99% of the samples, evaluated using 10-fold cross-validation.","PeriodicalId":256361,"journal":{"name":"J. Integr. Bioinform.","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128647779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}