Information Management for Material Science Applications in a Virtual Laboratory

Identification of Ligand Binding Site and Protein-Protein Interaction Area

“…When scienti fi c experiments are modeled The MACS lab experiments can be decomposed into three phases: the pre-processing phase for the extraction of and preparation of samples, the experimentation phase where the sample is processed using special devices, and the analysis phase where the collected experimental data is analysed by scientists (Frenkel et al 2001 ) following a work fl ow approach, the latter encode the logic of the experimentation processes and become an important resource to promote knowledge transfer among scientists. When scienti fi c experiments are modeled The MACS lab experiments can be decomposed into three phases: the pre-processing phase for the extraction of and preparation of samples, the experimentation phase where the sample is processed using special devices, and the analysis phase where the collected experimental data is analysed by scientists (Frenkel et al 2001 ) following a work fl ow approach, the latter encode the logic of the experimentation processes and become an important resource to promote knowledge transfer among scientists.…”

“…Hatched ovals represent operations, both executable and manual (Frenkel et al 2001 ) At a later stage, less experienced users can customize a given PFT such as in the MACS lab example, to perform a speci fi c experiment. The user then creates an instance of the PFT and modi fi es some parameters, de fi nes input and output data sources, attaches a new application work fl ow etc.…”

DROWNING IN DATA: Informatics and modeling challenges in a data‐rich networked world

“…Vast amounts of data and information are frequently entered into Laboratory Information Management Systems (LIMS) and e‐Lab Notebooks (electronic laboratory notebooks, ELN) (Paszko and Pugsley,2000), which are repositories of raw data. Important recent progress toward storing and managing such large data sets include the virtual laboratory (VL) project at the University of Amsterdam (Frenkel et al,2001), and XSIGMA (Kim et al,2006). However, most current LIMS and ELN solutions utilize database schemas, which often limit the capacity for the description of complex relations between information entities.…”

A Methodology for Integrating New Scientific Domains and Applications in a Virtual Laboratory Environment

“…The two initial application cases of VLAM-G were the DNA microarray application from the life sciences domain and the material analysis for complex surfaces application (MACS) (Frenkel et al, 2001) from the physics domain. The work described in this paper has been initiated and motivated by the need to support the requirements of both these initial application cases and any future applications within the VLAM-G.…”

“…• Large amounts of data are generated during experiments. For instance, material analysis experiments for complex surfaces typically generate 20 images per day where data size goes up to 100 MB per image (Frenkel et al, 2001).…”