Flow objects ============ yy Data objects ------------ CSDM .... Core Scientific Dataset Model is a lightweight and portable model and file format for multi-dimensional scientific data [ref to PLOS ONE paper]. EasyNMR handles NMR data in the CSDM format in its entire work processes. All other file formats, such as Bruker folder structures, are converted to CSDM before they are viewed or processed in EasyNMR. The CSDM data object contains a CSDM dataset that is read from a file or extracted from a folder. The properties window shows the Dimensions, Dependent Variables, and Global parameters. Dimensions describes the independent variables of the dataset. Dependent variables describe the experimental data. For example in a dataset of the type {X, Y} where X is the chemical shift at each point and Y is the intensity of the NMR spectra at each chemical shift, X is the independent variable described in Dimensions and Y is the dependent variable described in Dependent Variables. Global describes the pulse sequence, description, and all other NMR parameters – such as acquisition and processing parameters – that accompany your data, for example in a typical Bruker folder format. [Need to concisely explain the CSDM data format?] Table ..... The Table component allows the creation of a spreadsheet and exporting it through the File module. The user can edit the table (?). To create a table, you can use the Calculator module and use the add empty output button with the output type of ‘Table’. [Need help from @Thomas on this. This is as much as I know about Table and it may not be correct.] Text .... The text module allows adding rich text to your project. You can use this module to add descriptions or write notes. The text is visible in the ‘Text’ pane of description. To modify the text, click on Control to expand the Control pane, and then click on Edit. Now you can change the text. To apply changes, click on ‘Control’ again, and click ‘Done’. After you apply changes, the written text will appear in the Text pane and hides the editor. Remember: You can copy and paste rich text from/to other software to/from EasyNMR Text module. Note: You can change both text and its title. Molecule ........ The molecule object Function objects ---------------- Calculator .......... The Calculator module takes any input through the in (data) and par anchor and output either a CSDM or Table object. You can program the Calculation module in JavaScript. After programming, you can press the Calculate button to start computations. After performing computations, a green checkmark [Calculator with green checkmark] will appear in the project view. Simulation .......... The SIMULATION module allows you to perform numerical simulations of NMR experiments through the EasyNMR interface, especially numerical solid-state NMR simulations by SIMPSON [reference to SIMPSON papers here]. Simulations are performed on a backend server which hosts SIMPSON and communicates to EasyNMR. You need to be connected to the computation server using the eServer module to be able to run SIMPSON simulations on the computation server (see eServer module). SIMPSON input file is shown in the Input pane of the SIMPSON window. The Control pane allows your to have control over how the simulations run. For example, you can choose a Walltime, the maximum time for running simulations on the server, choose the Output Type, default CSDM. Press the Run button to send computations to the server. The status bar on the right shows the progress of the simulation. A green checkmark appears on the Simulation module icon when the computations are finished. The Type pane allows different types of computations in the future. The Log pane shows the output of SIMSPON simulation you last run on the server, similar to the command line prompts you would see if you had run SIMPSON on your local computer. The Output pane shows properties of the CSDM object that is exported from the Simulation module. Read this reference for a complete list of SIMPSON commands and Input file structure. Read this reference for a tutorial on using SIMPSON. Other resources on SIMPSON may be found in the following references. See the File module help for more information about the CSDM file format. Model ..... The model object eServer ....... The eServer allows running SIMPSON simulations on a computing server. You can access the eServer by ORCID authentication. After successfully logging in, you see the server you are connected to (fx. Server easynmr.nmrbox.org), its status (Status Running), your name (Name Armin Afrough), your ORCID number (ORCID 0000-0001-9923-2378), and the software accessible to this server (Capabilities simpson 4.2. 3_build16 peaks 0.1). You can log out from the server by pressing the log out button. SIMMOL ...... The SIMMOL object Trace ..... The trace object Plot .... The Plot module can plot data from single and multiple sources. All data can be arbitrarily combined to produce a single plot. Moreover, multiple data sets can be plotted simultaneously in a single plot module. A Plot module may be connected to several sources, such as CSDM and Simulation. In the Plot Layout pane, you can select the data source and its presentation. You can choose the Plot Type by clicking on the 1D [1D Plot Icon] or 2D [2D Plot Icon] icons. A list of data sets will appear that are connected to the Plot module and match the selected dimensions. You can check or uncheck the datasets in the list. Clicking on their checkbox activates their properties and you can modify their Color and Configuration (including Type: Lines/Markers/Lines and Markers, Linewidth, Title, and Scale; for Markers, you can modify the Point Size and Marker Color as well). Clicking on Configure X/Y Axis allows you to see and modify axis properties. You can make the axis Visible/Invisible, Reverse/Normal, Logarithmic/Linear, and with/without Zero Line. You can write labels for X/Y axis by entering a label in their Legend editbox. It is possible to change the axis units by choosing between Index/Quantity (frequency)/Dimensionless (ppm) options. The Plot pane of the properties window shows the plot with desired configuration with the possibility of zooming into the data. Zoom [Zoom Icon] and Pan [Pan Icon] allow accurate examining the plot. You can clock on Autoscale [Autoscale Icon] to return to the original view of the plot. Zoom in [Zoom in Icon] and Zoom out [Zoom out Icon] allow zooming in/out from the center of the view. You can download a PNG snapshot of the plot by clicking on the ‘Download Plot as a PNG’ button [Download Button as a PNG Icon]. High quality vector-format snapshots may be saved in the SVG format by clicking on ‘Download Plot as a SVG’ button [Download Button as a SVG Icon]. For peak picking of spectra, click on Peak Pick [Peak Pick Icon] and then drag a rectangle on the peak of interest. The mode of the peak will appear on the plot. Click on the Peak Pick icon again to deactivate the peak picking view. [More information about peak picking and integration by Thomas.] [Thomas helps with what is move legends. Does it rotate them to different corners?!] Auxiliary objects ----------------- File .... The file module allows you to download a copy of NMR data in CSDM format or to convert a table object into an Excel file. To save data as a file click on [file icon] to create a File module. Drag the File module to the desired place in the project view. Only certain components can be connected to the File module. Compatible modules include: CSDM, Table, SIMPSON. To connect the File module to a compatible component, click on [connect icon] and then on the anchor of the newly created File module. Anchors of other compatible components will blink. Click on the component of your choice. Remember: Always click on the connect icon [connect icon] to deactivate the connect tool after connecting desired modules. Remember: You can change the position of the anchor the left and right of an icon by clicking on the Anchors part of File module properties. Remember: For each module, you can see relevant help by clicking on ‘Documentation’ to expand it in the module properties window. Note: Components already connected to the File component will not blink. Configuration ............. The configuration object allows Transient objects ----------------- Folder ...... xxx Archive ....... yyy