modeldriven Architecture (MDA) advocates the use of models, rather than code, as the main development artifact. Yet model versioning and merging tools still lag in capabilities, ease of use and adoption relative to s...
详细信息
ISBN:
(纸本)9789897580659
modeldriven Architecture (MDA) advocates the use of models, rather than code, as the main development artifact. Yet model versioning and merging tools still lag in capabilities, ease of use and adoption relative to source code versioning and merging tools. This forces many teams to avoid model-based collaboration and concurrent model modifications. In this paper, we highlight the main challenges behind the relatively small adoption of model merging approaches. We present a novel model-based programming technology that addresses many of those challenges. The approach treats code and models uniformly, effectively enabling modelers to version and merge models using existing text-based technologies.
Background: In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory informati...
详细信息
Background: In recent years, the genome biology community has expended considerable effort to confront the challenges of managing heterogeneous data in a structured and organized way and developed laboratory information management systems (LIMS) for both raw and processed data. On the other hand, electronic notebooks were developed to record and manage scientific data, and facilitate data-sharing. Software which enables both, management of large datasets and digital recording of laboratory procedures would serve a real need in laboratories using medium and high-throughput techniques. Results: We have developed iLAP (Laboratory data management, Analysis, and Protocol development), a workflow-driven information management system specifically designed to create and manage experimental protocols, and to analyze and share laboratory data. The system combines experimental protocol development, wizard-based data acquisition, and high-throughput data analysis into a single, integrated system. We demonstrate the power and the flexibility of the platform using a microscopy case study based on a combinatorial multiple fluorescence in situ hybridization (m-FISH) protocol and 3D-image reconstruction. iLAP is freely available under the open source license AGPL from http://***/iLAP/. Conclusion: iLAP is a flexible and versatile information management system, which has the potential to close the gap between electronic notebooks and LIMS and can therefore be of great value for a broad scientific community.
Cancer progression is a complex process involving host-tumor interactions by multiple molecular and cellular factors of the tumor microenvironment. Tumor cells that challenge immune activity may be vulnerable to immun...
详细信息
Cancer progression is a complex process involving host-tumor interactions by multiple molecular and cellular factors of the tumor microenvironment. Tumor cells that challenge immune activity may be vulnerable to immune destruction. To address this question we have directed major efforts towards data integration and developed and installed a database for cancer immunology with more than 1700 patients and associated clinical data and biomolecular data. Mining of the database revealed novel insights into the molecular mechanisms of tumor-immune cell interaction. In this paper we present the computational tools used to analyze integrated clinical and biomolecular data. Specifically, we describe a database for heterogenous data types, the interfacing bioinformatics and statistical tools including clustering methods, survival analysis, as well as visualization methods. Additionally, we discuss generic issues relevant to the integration of clinical and biomolecular data, as well as recent developments in integrative data analyses including biomolecular network reconstruction and mathematical modeling.
暂无评论