Bioinformatics

Comparing Eukaryotic and Prokaryotic Translation The translation process is very similar in prokaryotes and eukaryotes. Although different elongation, initiation, and termination factors are used, the genetic code is generally identical. As previously noted, in bacteria, transcription and translation take place simultaneously, and mRNAs are relatively short-lived. In eukaryotes, however, mRNAs have highly variable half-lives, are subject to modifications, and must exit the nucleus to be translated; these multiple steps offer additional opportunities to regulate levels of protein production, and thereby fine-tune gene expression. A major difference between eukaryotes and prokaryotes is that, in a typical eukaryotic cell, protein synthesis takes place in the cytoplasm while transcription and RNA processing take place in the nucleus. In bacteria, these two processes can be coupled so that protein synthesis can start even before transcription has finished. The steps of protein synthesis...

  BioSPICE   Dashboard Bio-SPICE, an open source framework and software toolset for Systems Biology, is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells. In addition, our goal is to develop and serve a user community committed to using, extending and exploiting these tools to further our knowledge of biological processes.   BioUML BioUML is Java framework for systems biology. It spans the comprehensive range of capabilities including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization and simulations.   CADLIVE CADLIVE is a system for constructing large-scale biological networks (metabolic and gene regulatory networks) using GUI (Graphic User Interface) and saving them as regulator reaction equations in a database in the format compatible to a simulator. It has been deve...

Recall Depth-first Search (DFS), and Show that edge (u, v) is a)          a tree edge or forward edge if and only if d[u] < d[v] < f[v] < f[u] b)          a back edge if and only if d[v] < d[u] < f[u] < f[v]   c)          a cross edge if and only if d[v] < f[v] < d[u] < f[u]     Solution: By theorem, DFS of (undirected/directed) Graph let’s say G, where G= (V, E) and we have two vertices u and v such that they hold ·          Vertex u and vertex v are not successor of each other, and intervals d[u], f[u], d[v] and f[v] are disjoint. ·          Vertex u is descendant of vertex v and the interval d[u], f[u] is confined inside interval d[v] and f[v] ·          Vertex v , descendant of ve...