Playing around with CellNOptR Tool and MIDAS File

With CellNOptR, we will try to construct network models for the challenge. For this, the tool needs two inputs. First one is a special data object called CNOlist that stores vectors and matrices of data. Second one is a .SIF file that contains prior knowledge network which can be obtained from pathway database and analysis tools.

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Retrieving Data with AJAX using jQuery, PHP and MySQL

Last semester, I took a course from Informatics Institute at METU called “Biological Databases and Data Analysis Tools” where first we learned what is a database and how to do queries on it. Also, the technology behind databases are taught. Then, we learned many biological databases and data analysis tools available. These include gene, protein and pathway databases, tools for creating databases.

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Network Inference DREAM Breast Cancer Challenge

The inference of causal edges are described as the change on a node seen after the intervention of another node. If the curves obtained over time overlap (under intervention or no intervention), then there is no relation. Otherwise, we can draw an edge between those nodes and according to the level, up or down, the edge will be activating or inhibiting. These causal edges are context-specific so in different cell line data, we may have different relations.

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