User Manual Atom Mac
We recognize that Atom is still used by the community and want to acknowledge that migrating to an alternative solution takes time and energy. We are committed to helping users and contributors plan for their migration.
User Manual Atom Mac
This section describes how to start using AtoM once it has been installed. Itprovides a quick orientation to the home page, how to log in and log out, thevarious user roles in the system, the main page types a user will encounter, andhow to switch languages.
This section provides guidelines for searching, browsing, and navigating. Mostof the functions discussed are available to all user roles,including researchers with read only access. However,some navigation features (e.g. edit mode), are only available to users withedit access privileges.
Electronic versions of these documents allow you to quickly get to the information you need and print only the pages you want. The Intel 64 and IA-32 architectures software developer's manuals are now available for download via one combined volume, a four volume set or a ten volume set. All content is identical in each set; see details below.
At present, downloadable PDFs of all volumes are at version 078. The downloadable PDF of the Intel 64 and IA-32 architectures optimization reference manual is at version 045. Additional related specifications, application notes, and white papers are also available for download.
Using ForkLift will come very easily. If you are used to Finder, everything will look familiar, and all the extra functionality will work as you expect it. ForkLift's user interface has got highly modular by now. You can have it anyways, from a minimal single pane look to the pedal-to-the-metal 3 ton engineering monster it can become, depending on what you need at the moment.
You need three basic information to connect to a remote server: server hostname, username, and password. Once connected to the server, you will be able to work with the data stored on the server in the same way you work with local data. You can use Quick Look, you can edit files, browse archives or use batch rename.
Cloud Files is a cloud hosting service that provides "unlimited online storage and CDN" for media (examples given include backups, video files, user content) on a utility computing basis offered by Rackspace. Use your username and API Key to connect.
Network File System (NFS) is a distributed file system protocol allowing a user on a client computer to access files over a computer network much like local storage is accessed. To connect to an NFS share click choose Go > Connect from the menu or use the shortcut Command-K, choose NFS protocol, enter the URL of the share and click on Connect.
The manual is written in AsciiDoc and includes some extra files which are generated from the source code. Run cargo test and cargo test -p xtask to create these and then asciidoctor manual.adoc to create an HTML copy.
For more information on how to set up LSP mode and its extension package see the instructions in the LSP mode manual.Also see the rust-analyzer section for rust-analyzer specific options and commands, which you can optionally bind to keys.
For some resources, there is no user/app context. These are resources that affect data input, indexing, or deployment activities. Index-time resources are considered system configurations. These resources are available from servicesNS endpoints.
Because there is no user/app context, user-specific settings are ignored. Access to resources is based on the capabilities defined by the user role. For example, /data/inputs/monitor looks the same to all users who have access to the resource. User role determines access rights.
For users with administrator privileges and machines MacOSX version 10.5 or higher: Download the ncbi-blast-2.2.18+.dmg installer and double click on it. Double click the newly mounted ncbi-blast-2.2.18+ volume, double click on ncbi-blast-2.2.18+.pkg and follow the instructions in the installer. By default the BLAST+ applications are installed in /usr/local/ncbi/blast, overwriting its previous contents (an uninstaller is provided and it is recommended when upgrading a BLAST+ installation).
The Atom Properties list describes the characteristics of a selected atom. These characteristics include the identifying traits such as element, what residue:Mol:Object it is a part of, and where it is located. Further characteristics place it within the context of the molecule being displayed under the section Bonds. Finally, there is a section containing 3 items: Marked Distance, Marked Angle, and Marked Dihedral. These are types of measurements we will use in Chapter 6.2.
The Top Menu will look familiar to users who use the Microsoft suite of programs or most modern productivity software. The 8 top-level categories are shown in the green box in Figure 2.5. We will explore several of this categories in more depth in later chapters. One note to make now is that the Analyze category is inaccessible until a molecule is loaded. This is shown as being in light grey, compared to the black of other categories. In general, if a menu category or option cannot be used under the current conditions, it will be colored grey.
While not formally part of the help system, users can click on the Help category in the top menu and then choose Play Help Movie (Help>Play Help Movie) to access YASARA rendered movies introducing users to a variety of topics. The movies are interactive and useful for first-time users, however they are not searchable and can take a while to find a specific topic. Therefore, I recommend going through the help movies once or twice early on, but using SearchDoc as you become more experienced.
By default, Nuclide does not install all of the recommended Atom packages that enhance the Nuclideexperience. This was done purposely in order to ensure that users have to opt-in to some featuresrather than obtrusively modify their work environment.
The results of all object searches is a table containingthe names of all objects that satisfy the search, with hyperlinks to theircorresponding data pages, along with any additional columnsrelevant to the particular search. The table will initially be sortedalphabetically by name, but small triangles in the column headersallow the user to sort by any column, in either ascending ordescending order.The sections below describe the different search criteriathat are available for each object type.
In graph mode, the entire track is assigned a color from a predefinedset of colors. However, it is possible for the user to choose thecolor of a track, by adding a new header comment line close to the topof the GFF file, before uploading the file. An example line lookslike this:
The Pathway Tools Omics Dashboard is a tool for visualizing omicsdata. It facilitates a rapid user survey of how all cellular systemsare responding to a given stimulus. It enables the user to quicklyfind and understand the response of genes within one or more specificsystems of interest, and to gauge the relative activity levels ofdifferent cellular systems. The dashboard also enables a user tocompare the expression levels of a cellular system with those of itsknown regulators.The dashboard consists of a set of panels, each representing a system ofcellular function, e.g. Biosynthesis. For each panel, we show a graphdepicting omics data for each of a set of subsystems,e.g. Amino Acid Biosynthesis and Carbohydrates Biosynthesis. Eachpanel has its own y-axis, so that omics data for the differentsubsystems within a panel can readily be compared with each other.Multiple timepoints or experimental conditions are plotted asseparate data series within the graph.Clicking on the plot for a given subsystem brings up adetail panel, breaking that subsystem down further into its componentsubsystems. At the lowest level, the values along the x-axiscorrespond to the individual objects in the dataset (i.e. genes forgene expression data, metabolites for metabolomics data, etc.). Fromthis level, you can also view the relevant pathway diagrams overlaidwith omics data, operon diagrams, and, for transcriptomics data, theexpression levels of relevant regulators.
The Cellular Overview diagram depicts the biochemical machinery ofan organism as described in a PGDB. Each node in the diagram (such asthe small circles and triangles) represents a single metabolite, andeach blue line represents a single bioreaction. This page describes the organization of the Cellular Overview and the operations users can performto interrogate it. Different PGDBs will have different components ofthe diagram present or absent depending on what was included by thePGDB authors.Note: The Cellular Overview has been tested on Firefox 59.0, Safari 11.1, and Chrome 65.0.
Note for Mac users with a one-button mouse: left-click isthe usual click, and right-click is the Mac control-click (i.e., youhold down the control key and click). But the exact keys can becustomized on your Mac via the system preferences panel.
The Pathway Tools Omics Viewer uses the Cellular Overview for anorganism to visualize data from high-throughput experiments in aglobal metabolic pathway context. The input to the Cellular OmicsViewer is a set of gene, protein, and/or reaction names oridentifiers, and data values for each gene, protein, and reaction.The Omics Viewer generates a new version of the Cellular Overview inwhich the reaction steps identified by the input genes, proteins, andreactions are colored according to the provided data values. Forexample, for a gene expression experiment, the software identifies thereactions catalyzed by the product of each supplied gene, and colorsthat reaction with a color value computed from the data point providedfor each gene. The data values in the provided dataset are mapped toa spectrum of colors. Similarly, for metabolomics experiments,compound nodes in the Cellular Overview are colored according to thedata values for the specified compounds. This facility enables theuser to see which pathways are active or inactive under some set ofexperimental conditions. 350c69d7ab