About this app

Life as we know it has continued to shock and amaze us, consistently reminding us that truth is far stranger than fiction. Euplotid is a quantized geometric model of the eukaryotic cell, a first attempt at quantifying, using planck's constant geometric shape as its base, the incredible complexity that gives rise to a living cell. By beginning from the very bottom we are able to build the pieces, which when hierarchically and combinatorially combined, produce the emergent complex behavior that even a single celled organism can show. Euplotid is composed of a set of quantized geometric 3D building blocks and constantly evolving bioinformatic pipelines encapsulated and running in Docker containers enabling a user to build and annotate the local regulatory structure of every gene starting from raw sequencing reads of DNA-interactions, chromatin accessibility, and RNA-sequencing. Reads are quantified using the latest computational tools and the results are normalized, quality-checked, and stored. The local regulatory neighborhood of each gene is built using a Louvain based graph partitioning algorithm parameterized by the chromatin extrusion model and CTCF-CTCF interactions. Cis-Regulatory Elements are defined using chromatin accessibility peaks which are then mapped to Transcription Start Sites based on inclusion within the same neighborhood. Deep Neural Networks are trained in order to provide a statistical model mimicking transcription factor binding, giving the ability to identify all TFs within a given chromatin accessibility peak. By in-silico mutating and re-applying the neural network we are able to gauge the impact of a transition mutation on the binding of any transcription factor. The annotated output can be visualized in a variety of 1D, 2D, 3D and 4D ways overlaid with existing bodies of knowledge, such as GWAS results or PDB structures. Once a particular CRE of interest has been identified by a biologist the difficulty of a Base Editor mediated transition mutation can be quantitatively observed and induced in a model organism

App Permissions

Allows applications to open network sockets.
Allows an application to write to external storage.
Allows applications to access information about networks.
Allows using PowerManager WakeLocks to keep processor from sleeping or screen from dimming.
Allows applications to access information about Wi-Fi networks.
Allows an application to modify global audio settings.
Allows access to the vibrator.
Allows an application to read from external storage.