Details

A core signaling component of the notch network + a molecular interaction database accessible through an online VLSIC-like interface

by 1977- Barsi, Julius Christopher

Abstract (Summary)
37 For the most part, each subcategory is self-explanatory. However, I will briefly explain subcategories with variable parameters or those instances where a subcategory’s content cannot be directly inferred from its title. Both, ‘Component Type’ (i.e. receptor) and ‘Compartment’ (i.e. cytoplasm) hyperlink out so as to reveal all other components of the same type or those that reside within the same compartment, respectively. ‘Chromosomal location’, displays the genomic location for any given component in physical terms (chromosome number and base pair range) in Mus musculus and hyperlinks out so as to view the location with Ensembl Mouse ContigView. ‘Amino acids’, in addition to displaying the number of residues for any given component, hyperlinks out to the Geneatlas: Gene Database. In order to facilitate the analysis of network topology and/or predict repercussions throughout the network, I created a subcategory labeled ‘Linked Components’. This in turn, is further subdivided in two. The first, labeled ‘Directly Connected’, identifies all immediate neighbors of a given component. Whereas the second, labeled ‘n Level Indirect’, enables the user to choose the level of indirectly connected components displayed. In as far as data per se is concerned; each ‘Image’ expands so as to reveal a full resolution image of the relevant data. Finally, the ‘PubMedID’ subcategory hyperlinks out so as to reveal the corresponding paper as indexed by PubMed. However, if the user is logged on to the Artzt laboratory web site, an additional hyperlink becomes visible, by which the user may directly download the paper as a PDF. Administration One of the main factors behind this endeavor was to create a format in which a model can be amended as new data becomes available. The nature of the database is such, that only minimal effort is required for its upkeep. Though most issues have been addressed so as to facilitate this process, the database is not, nor was it ever intended to be automated and hence, requires a curator. The latter, whether a single individual or a team, is granted administrative privileges via a secure login < http://web.biosci.utexas.edu/artzt_lab/admin/login/login.aspx > accessible from any 38 computer with an active internet connection (Figure 24a). The fact that most modifications to the database can be made online simultaneously by different administrators, further streamlines this process. Upon successful login, the curator is directed towards the administrator portal (Figure 24b); from which four distinct web pages can be accessed. These pages allow all aspects of the database per se to be modified at will (Figure 25). There is one feature whose modification remains unavailable by hyper text transfer protocol (http), that of the Macromedia Flash Player enabled interface. Once modified however, this can easily be updated through a file transfer protocol (ftp) connection. Analytics In an effort to assess the response generated by the Murine Notch Signal Transduction Database, statistics regarding internet traffic were gathered during the spring semester of 2006 (specific range: 01/01/2006 00:00:00 – 05/08/2006 11:40:28). During this time, the database had been accessed a total of 23,578 times. For comparative purposes, the Artzt laboratory home page was visited only 588 times within the same time frame. The average time spent on the database was 00:07:27; however interpretation of this value is limited. 71.64% of the users were confirmed to be accessing the database from within the United States. Perhaps of more significance is the fact that 391 distinct users [as defined by their internet protocol (IP) address and further authenticated through cookies] accessed the database recurrently with session lengths lasting a minimum of 00:30:00. I am fully aware that from these statistics one cannot accurately judge the level of success (or lack thereof) of the database. Nonetheless, the numbers are encouraging.
Bibliographical Information:

Advisor:

School:The University of Texas at Austin

School Location:USA - Texas

Source Type:Master's Thesis

Keywords:notch genes mice

ISBN:

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