![]() ![]() Download and open the text file with the data described above. Go to the menu Apps → Omics Visualizer → Import table from file. Start Cytoscape or close the current session from the menu File → Close. An adapted and simplified table with the data from this study is available here. Each protein can have multiple significantly regulated phosphorylation sites, each of which is associated with two log-fold change values (one for each control tissue), a Benjamini–Hochberg adjusted p-value, and a cluster assignment that groups sites with similar behavior across samples. ![]() The study used mass spectrometry to compare the phosphoproteome of primary cells derived from epithelial ovarian cancer (EOC) to those of two healthy tissues, namely distal fallopian tube epithelium (FTE) and ovarian surface epithelium (OSE). We will work with phosphoproteomics data from an ovarian cancer study ( Francavilla et al., 2017). In this exercise, we will load a data table with proteomics data, filter it, retrieve a STRING network for the proteins, and visualize site-specific information onto the protein network. Similarly, make sure you have the stringApp, enhancedGraphics, and their dependencies installed before closing the App Manager. Search for the Omics Visualizer in the search field if it is not already installed, select it and press the Install button to install it. The exercises require you to have certain Cytoscape apps installed. Then start Cytoscape and go to Apps → App Manager to check for new apps, install them and update the current ones if necessarily. To follow the exercises, please make sure that you have the latest version of Cytoscape installed. visualize time-series data onto networks.visualize site-specific data onto networks.To learn more about this approach, please, read about our research framework, ecological thinking and cognitive variability methodology.In these exercises, we will use the Omics Visualizer app for Cytoscape to retrieve molecular networks from the STRING database and visualize site-specific information on the nodes. We aim for a dynamic non-equilibrium that takes you through a variety of different states, each beneficial for a certain part of research process. underlying nuance) and intent (focusing vs. It does so through encouraging variability in scale (high-level ideas vs. InfraNodus modulates this process, helping you balance between openness and coherence. Moments of growth are followed by saturation and decline, which is an opportunity for optimization and reorganization. the context) and the resources (attention, data, knowledge). We see thinking as an ecological process closely related to ecosystem (i.e. InfraNodus can be used as a mind antivirus against obsessive loops - biased ideas, mundane patterns, totalitarian thinking, propaganda, and narrow-mindedness - proposing a kind of thinking that is pan~archic: spanning a range of states and modalities. Too often people get stuck with a certain idea or a pattern of thinking. InfraNodus is specially designed to promote cognitive variability. We also provide an API to ensure that this way of thinking is available not only to humans, but also to other machines, applications, AI programs, and machine learning algorithms.Ĭognitive Variability: Panarchic Thinking with InfraNodus If you are interested to support our work, you can sign up, learn more about our philosophy, and join our team. This can be very helpful for reading, writing, scientific research, and marketing studies. Our research shows that network representation helps avoid cognitive bias and encourages connecting ideas in new ways. Based on this representation, you can enhance your perspective of any discourse and explore the nuances of meaning that would not otherwise be available. InfraNodus represents ideas as a network, so you can discover relations and patterns within. It is made to promote ecological dynamics and diversity on the cognitive level. InfraNodus is a tool that is developed to help you think this way. It can discover the obvious, but it can also reveal the things that are hidden and ponder the gaps that have not yet been bridged. It embraces diversity, but it can also obsess over one thing when needed. What is a mind that is ecological? It has the ability to have an overview, but it can also zoom into any idea. Gregory Bateson coined a beautiful term: "ecology of the mind". AI-Assisted Thinking & Insight Generation:
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