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LAMINA - Leaf shApe deterMINAtion

Andreas Sjodin on Jul 27, 2011
LAMINA

Featured software from colleagues: further development of the MASQOT code base

An increased understanding of leaf area development is important in a number of fields: in food and non-food crops, for example short rotation forestry as a biofuels feedstock, leaf area is intricately linked to biomass productivity; in paleontology leaf shape characteristics are used to reconstruct paleoclimate history. Such fields require measurement of large collections of leaves, with resulting conclusions being highly influenced by the accuracy of the phenotypic measurement process.

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MASQOT & MASQOT-GUI

Andreas Sjodin on Jul 27, 2011
MASQOT-GUI

cDNA microarray technology has emerged as a major player in the parallel detection of biomolecules, but still suffers from fundamental technical problems. Identifying and removing unreliable data is crucial to prevent the risk of receiving illusive analysis results. Visual assessment of spot quality is still a common procedure, despite the time-consuming work of manually inspecting spots in the range of hundreds of thousands or more.

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UPSC-BASE

Andreas Sjodin on Jul 27, 2011
Digital Northern

The increasing accessibility and use of microarrays in transcriptomics has accentuated the need for purpose-designed storage and analysis tools. Here we present UPSC-BASE, a database for analysis and storage of Populus DNA microarray data. A microarray analysis pipeline has also been established to allow consistent and efficient analysis (from small to large scale) of samples in various experimental designs. A range of optimized experimental protocols is provided for each step in generating the data.

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PopGenIE

Andreas Sjodin on Jul 27, 2011
PopGenIE

A dramatic shift has been seen in biology during the last decade. Modern biology has entered a genomic era with new genomes being sequenced at an ever-increasing speed. High-throughput technologies allow the simultaneous measurement of thousands of characteristics in biological systems such as proteins , metabolites, and RNA . The amount of public data available has open possibilities to study thousands of genes at the same time. This drift from a univariate view of biology to systems biology demands totally different competences from researchers.

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