Have a properly configured and running Galaxy instance.In order to process the user's data we need to PeptideShaker Online use this ability to coordinate different Galaxy tools in order to process complex data and give the results back to the frontend to be shown to the user in the best possible way independently of Galaxy's own interface. Galaxy's main contribution has been to establish a common framework in which different applications (called "Galaxy tools" in Galaxy context, which may be written in different programming languages, with different dependencies and requirements) can work together transparently to the user. Galaxy is an open source, web-based platform for data intensive biomedical research. ℹ️About GitHub Wiki SEE, a search engine enabler for GitHub WikisĪs GitHub blocks most GitHub Wikis from search engines.As its developers state in the main Galaxy web portal: A) Interactive spectrum viewer where the user can zoom in or out and use all the features including denovo sequencing.The "Peptide-to-Spectrum Matches" tab consists of the following: Upon selecting the interesting peptide, the "Peptide-to-Spectrum Matches" tab will be activated and the user can navigate to it. Here the user selects a peptide from the protein-peptide network or protein coverage table in order to see the peptide and spectrum details at the Peptide-Spectrum Matches level. C) Protein coverage table with the peptides and their location.B) Protein 3D structure (using LiteMol).A) Protein-peptide mapping (or proteoform-based on information from Reactome).The "Protein Visualization" tab includes the following: Upon selecting the protein (group), the "Protein Visualization" tab will be activated and the user can navigate to it. The user filters the dataset at the Dataset Overview level to find and select a protein (group) for closer inspection at the Protein Overview level. H) Protein table with the currently filtered results.E) Number of peptide-to-spectrum filter.C) Post-translational modifications filter.B) Chromosome filter (requires the use of a UniProt-based FASTA file).A) Protein inference and protein validation filters.The users select the wanted dataset from the "Projects Overview" tab, which automatically displays the "Dataset Overview" the tab containing the following information: Users have to upload FASTA, Proteins, and Peptides files. Users can also upload and visualize their own processed data files using the Upload Your Own Project Files tab located under the Visualize Data tab. Please note in order to support the 'chromosome mapping' filter feature, the FASTA files need to be a UniProt-based FASTA file. When a user has successfully logged in with their private API key, they can upload their own FASTA files and spectrum files through the Search tab.Ĭurrently, the supported spectrum input formats are mgf and mzML for identification and Thermo raw files for both identification and quantification. Once you click the "Login" button you will be returned to the main PeptideShaker Online page logged in with your Galaxy user ready to use all of its features. Once the main PeptideShaker Online page is shown, click the bottom-right button called "Galaxy Login" and enter the previously generated API Key. Please keep this key in a safe place and then open the PeptideShaker Online website with your browser. This can be easily done when logged in with your user, accessing your user preferences, and clicking "Manage API Key" - "Create a new Key". API keys allow the use of your Galaxy user account programmatically without sharing your private password. Once you have registered your user using the register user form of your Galaxy GUI instance (please note that this user should not be the same as the user configured for managing the Galaxy instance, and in this case should not have admin permissions), you can generate an API key for it. So, apart from testing purposes, it is highly recommended to use a specific user in order to have your own data history and be able to execute tasks associated only with your user. Although PeptideShaker Online allows you to execute tasks anonymously, your data will then be shared with anybody using the application. Before you start using PeptideShaker Online, you will need a Galaxy user API key.
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