Computational Team

G-nome Surfer Pro is written in C# for the Microsoft Surface using the Surface SDK. State is managed using the ViewModel system and time consuming processes, like retrieving publications and running BLAST, are run in threads behind the main UI thread.

After selecting a genome from the tree menu the chromosome bar is populated with genes from the GenBank file. Another genome can be selected at anytime from the pull down search menu.

The chromosome bar is infinitely scrolling and position on the chromosome bar is tied into the orientation of the chromosome wheel through the view-model system allowing manipulation of one to affect change of the other. GenBank files are parsed for sequence, translation and any notes, all of which are available as information objects, which are accessible from any gene on the bar.

Information from any gene’s GenBank file are viewable as “ScatterViewItem” objects which can be moved and re-sized on the main “ScatterView” workspace. Users can view and annotate sequence/translation information by dragging and overlaying one over the other. All information objects can be moved to and from the extended desktop by dragging or tossing or erased by tossing them off the sides of the workspace. By moving objects between ScatterViews, users can view and organize data in a distraction free environment which can be pulled up over the main workspace or hidden from view.

Publications are populated in a scrollable list and can be dragged and dropped from the listBox to the main workspace or extended desktop through manipulation of the objects template. The PubMed search results for the gene are fetched and parsed for abstracts, authors, and publication data.


In the Primer Genie workspace, alignment results are generated using an algorithm .jar written by the software team, and BLAST results are generated using the NCBI BLAST software. Both are accessed from the command line, with BLAST results being written to file and parsed out for display and alignment results being pulled from common output for further calculation for hetero-dimer and self-dimer tests.

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Ethical User Study practices:

Overview: G-nome Surfer Pro

Hypothesis Forming

G-nome Surfer Pro is an integrated environment for viewing prokaryotic genomic data and literature. Users can find genes on the chromosome wheel or search for a gene name or Genbank number(?), access Genbank notes and publications from Pubmed and view alignment and translation from the chromosome bar. The extended desktop provides distraction free workspace for information processing and hypothesis formation. The Microsoft Surface allows users to collaborate in pairs and teams on design and research tasks

Genes can be taken directly into the Primer Genie designer for primer design. In the Primer Genie workspace users can perform alignment related tests, BLAST and save designs as BioBricks. The system is designed for integration with the Clotho database.

Demo Video

Wetlab

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Safety practices:

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