Adagio User’s Manual Catalog No: 78-8000 phone:508.429.6809 email: info@kdscientific.com web: www.kdscientific.
TABLE OF CONTENTS INSTALLING ADAGIO ......................................................................... 4 1.1. SYSTEM REQUIREMENTS ......................................................... 4 1.2. Installing The Software .............................................................. 4 2. PUMP NETWORKS AND MODELS ............................................ 6 2.1. Compatible Network Topologies ............................................... 6 2.2. Compatible Pump Models................................
5.2. Method Execution Control ....................................................... 42 5.2.1. Starting, pausing, resuming and stopping methods .......... 42 5.2.2. Runtime execution information.......................................... 43 5.2.3. Controlling special situations during the Method execution44 5.2.4. Method Progress window.................................................. 44 5.3. Method Data Logging............................................................... 46 5.3.1. Excel report..........
INSTALLING ADAGIO Before using Adagio, check the system requirements and then install the software onto your hard drive. 1.1. SYSTEM REQUIREMENTS Although Adagio is an easy-to-use software method, the processing of the data requested and generated by the pumps mobilizes an important amount of PC resources and can be highly time-consuming if the computer used is not powerful enough. We recommend the use of a computer that meets the following minimum requirements: 1) 2 GHz Pentium® processor or higher.
Press the Next button to move to the Destination Location screen. Select the location that you would like Adagio to be saved on your PC then press Next. In the specified location, Adagio will download an executable file and a reference database. Once successfully installed, you will have the option to run Adagio immediately. To do so, click the dialog box ‘Run Adagio Now’ and then press the Finish button.
2. PUMP NETWORKS AND MODELS Adagio is able to communicate with a pump connected to a computer by means of a serial / USB communications protocol. 2.1. Compatible Network Topologies The following pump network topologies can be controlled by Adagio: • Direct Connection: Each pump is connected to a single serial / USB port. • Daisy-chain: A single pump is connected directly to the computer and the rest of the pumps are sequentially “chained” to the previous one.
Adagio is compatible with the following pump software versions and any newer revisions: 2.3. Legato 200 v1.0.2 Legato 100 v1.0.1 Pump Communications Protocols Adagio is responsible for selecting and fulfilling the communications protocol suitable for each pump with which it will communicate. The communications protocol of each model that the application will utilize is described in the pump’s corresponding user’s manual.
Flow chart outlining how to run Adagio 3. DEFINING PUMPS Open the Adagio software by double-clicking on the corresponding icon in the Windows® desktop. An initial blank screen will be opened.
Before using the rest of the application functionalities, Adagio must establish communication with any pumps that will be controlled by the software. To open the Pump Configuration window, click on the Configure Pumps button located at the top of the screen. When the Pump Configuration window is first launched Adagio will automatically check for connected pumps. If a pump is detected the Pump Configuration Assistant will launch. (see section 3.1.
Note that if you close and restart Adagio, pumps connected via a USB cable may re-establish communication through a different COM port than was previously defined. Therefore, if multiple pumps are defined they could potentially change COM ports during a re-start. Be sure to verify which pump you are communicating with before running a Method. Except for “green” status, the row color (text foreground color) coincides with the status icon color in order to facilitate its visual identification.
Pressing the Refresh button of the window updates the status of all the currently defined pumps. To do that, the application establishes communications with each of the defined pumps in order to determine their current availability (that is, whether they are currently connected to the computer or not) and to obtain their corresponding pump model. When connecting a new pump model, use the Add new… function. Do not attempt to edit an existing connection for a new pump model.
Enter the following parameters and then press the Next button: • Pump Name (required): The name that will be shown when the pump is referenced within the rest of the application’s functionalities. Pump names must be unique so that two different pumps (that is, two pumps with different connection details) do not have the same name. • Pump Serial Number (optional): The serial number that will be assigned to the defined pump. The default pump serial number for new pumps is empty.
• Pump Address: The address number assigned to the pump within the communications chain. The default pump address number for new pump is one more than the highest address within the previously defined pumps in the same chain (that is, configured with the same COM port) or 0 if the first pump is being defined. If the Pump Configuration Assistant was launched to modify an existing pump, fields will contain the previously entered information for that pump.
Press the Start identification button to determine the pump model connected to the serial port with the address number specified in the previous step. An activity bar serves as a visual signal of the progress of the identification process At the end of the identification process, the assistant shows the result indicating the detected pump model name and version. The automatic identification process requires the pumps to send the version identifier.
The rack model list will show all of the rack models compatible with the detected pump model. A specific pump model must be selected in order to finish the identification process. This information will be used to determine the maximum number of syringes that are mountable on the pump and the maximum size of these syringes. These values are later used in the method definition to validate the maximum number of syringes and maximum size of the syringes that can be used.
The Syringe Model Selector contains the list of mountable syringe models within the selected pump model (both standard and custom syringe models). By default, the first syringe model in the list is selected. When a syringe model is selected, its diameter is shown and the flow range of the pump is automatically calculated (and displayed) based on the speed range of the pump model and the syringe diameter.
3.4. Defining Custom Syringe Models In addition to the pre-configured syringe models, Adagio allows you to define your own custom syringe models. The Custom Syringes window is available through the Configuration menu option with the same name. Under Configuration choose Custom Syringes to bring up the following window: The Custom Syringes window shows a list of custom syringe models that have been defined. These syringes are available within the rest of Adagio’s functions (such as Method creation).
The Custom Syringe window also includes a toolbar with the following buttons: • Add: Launches the editor tool in order to define a new custom syringe model. • Edit: Launches the editor tool in order to modify a previously defined custom syringe model. This button is enabled when one (and only one) syringe is selected. A double-click on a row of a defined custom model automatically launches the editor tool (see 3.4.1). • Remove: Requests confirmation to remove the selected custom syringe models.
4. DEFINING METHODS Methods are the procedures by which a set of pumps execute a sequence of pre-defined steps and thus a particular flow rate is applied. Adagio allows you to manage your own methods through the Methods Definition window which is accessed by means of the Define Methods button located in the experimentation assistant bar: The Methods Table shows the list of methods already defined.
A double-click on a row of a method automatically launches the Method Editor tool (see 4.2. for more details). The Methods Definition window also includes a toolbar with the following buttons: • • • • Add new: Launches the Method Editor tool in order to create a new method. Edit: Launches the Method Editor tool in order to modify an existing method. This button is enabled when one (and only one) method is selected.
4.2.1. Method name, description and dates To create a new method click the Define Methods button located on the experimentation assistant bar. In the Methods Definition window press the Add New button to bring up the Method Setup window. Enter a unique name for the method. In order to facilitate the exportation and importation tasks (see 4.3) the method name only allows the same characters that are allowed for a file name. A method description of up to 255 characters can also be entered.
4.2.3. Number of syringes, syringe model and flow units selection Once a pump model and a rack model are selected, a syringe model must be selected among the list of compatible models. A syringe model (either standard or custom) is considered “compatible” with a rack model when the rack model can hold syringes with a capacity equal to or higher than the syringe model’s capacity.
4.2.4. Flow evolution graph: steps and flow definition The Flow Evolution Graph area shows a graphical representation of the defined method’s steps. It works as a “canvas” in which you can “draw” your own step sequence and the desired flow rate evolution lines. The flow evolution chart area provides a toolbar to facilitate the execution of the most common tasks related to the method edit process.
The flow evolution graph also provides a contextual menu which is dropped down when the right mouse button is pressed over the graph area. This menu facilitates the access to the following options: • • • • • Properties … Insert Concentration wizard: See 4.2.4.13. for more details on this option. Delete Link to previous step: See 4.2.4.6. for more details on this option. 4.2.4.1.
Y-axis (flow) End flow marker Expected flow evolution line Start flow marker Step block X-axis (time) Step block Step block Duration marker The first step block is always located at the left most side of the graph plot. As no time gaps are allowed between two steps, the following blocks will be drawn next to the previous one. Step blocks can be easily selected by clicking on them with the left mouse button (when in selection mode). 4.2.4.2.
Y-axis has the following characteristics: • • • • • • Values will be measured and shown in the flow units selected by you. The maximum value (always positive) will be determined by the maximum flow between those defined by you within the steps of the method. It will be also limited by the maximum flow allowed by the selected pump and syringe models (see 4.2.3). The maximum flow will be represented by a horizontal line with a tag showing the value. The area above this maximum flow will be shaded gray.
4.2.4.3. Status bar information A status bar located on the bottom of the flow evolution chart shows the following information when the mouse pointer is moved over the graph area: • Time: corresponding to the horizontal position in which the mouse pointer is located. It is shown in time format (hh:mm:ss). • Flow: corresponding to the vertical position in which the mouse pointer is located. The flow unit value is formatted depending on how many digits are accepted by the pump model.
4.2.4.5. Adding new sequential steps to the Method • The Add button of the toolbar sets the graph into “addition” mode. When the graph is set to “addition” mode, new steps can be easily appended to the method. To add a step, click in the blank area of the flow evolution graph. Each click will create a new step (and its corresponding step block) with the following information: Check the graph’s scale before adding steps. To adjust the scale use the buttons.
When adding a new step the Step Editor window will automatically open, allowing you to edit the step’s target values (duration, flow values and step linkage property). This window can also be accessed by clicking on the Properties icon in Method Setup or by right-clicking on a step and selecting ‘Properties…’ Changing the flow may affect the duration or volume of the step.
4.2.4.6. Changing the properties of a step The following properties of a defined step may be changed using the flow evolution graph’s visual elements: • Duration: change by dragging the duration marker along the X-axis. Whenever the mouse pointer is located near to the duration marker, it automatically changes to a horizontal double arrow pointer. The duration marker is prevented from being dragged before the step’s start time.
4.2.4.7. Inserting steps into a method The Insert button of the toolbar (and its equivalent option within the contextual menu of the selected step) allows you to add a new step just before the currently selected step. This button is enabled when a step is selected and when the total quantity of steps has not reached the predefined limit of the selected pump model as described in 4.2.4.5.
In Case 2 (in which the selected step is not linked to the preceding), the inserted step is not linked either, but the selected step changes its linking property to be automatically linked to the inserted. Finally, the inserted step is automatically selected and the method is recalculated so that its overall information is updated within the status bar (see 4.2.4.3. ). 4.2.4.8.
Steps within a loop cannot be edited while the loop is enabled. To edit a step, disable the loop, make the desired changes and then re-enable the loop. 4.2.4.10. Protecting the pump against forced flow rates Adagio does not consider the maximum forces applicable to each of the pump models. You must configure the pumps to prevent them from going beyond their maximum forces through their own user interfaces. 4.2.4.11.
4.2.4.13. Concentration wizard A Concentration Wizard is available to facilitate the task of designing a step sequence (or a single step) from a known target concentration and dose. This tool is accessible both through the flow evolution toolbar and from the Concentration Wizard … option in the contextual menu of the chart. The following information must be entered to set up a concentration step: • Animal weight: the weight (always in Kg) of the subject to/from which the fluid will be infused / withdrawn.
The number of doses, dose value and lag time fields are available only if the “Multiple Doses” option is selected. This means that a step sequence is to be built from a known dose and concentration. The duration value field is available only if the “Single Dose” option is selected. This means that a single step is to be built from a known concentration and duration.
Flow rate (ml/min) Flow rate V (ml) Step 1 • V (ml) Step 2 Lag time Step 3 Duration: a single step is inserted with the given duration and flow rate. If the window is closed by pressing the Ok button, a data verification process is automatically executed checking that: • • • • • • Subject weight > 0 kg Flow rate is within the flow range of the Method (see 4.2.
4.2.4.14. Accepting and cancelling a method edit When the Accept button is pressed within the Method Editor, it is closed and the changes done within the method are stored in the application’s configuration. However, a previous information integrity check is carried out in order to avoid an inconsistent method being created. The checks considered are the following: • • • • Method name duplication: as stated in 4.2.1, the method name must be unique. A pump and rack model must be selected.
4.3. Importing and Exporting Methods Defined methods can be saved into external files so that they can be loaded on a different PC (or on the same PC, for example, in case it should be recovered from a data loss). Please note that the storing and retrieval options are related to the PC and not to the pump devices. When the Methods Definition Window is open, Import and Export commands can be found under the main File tab.
If a method file could not be read or its internal structure does not match with the expected, the application warns you, the method file is ignored and the importation process continues with the next selected file. When the importation process finalizes, the open dialog is closed and the method table within the Methods Definition window is automatically updated.
5. EXECUTING METHODS Methods defined with Adagio can be executed within the configured pump system. To do that, a floating window called Method Execution is provided through the Execute Methods button located in the experimentation assistant bar. The available pump list table shows the pumps already defined within the pump system together with the method to be executed within each of them.
A double-click on a row which has both a pump and a Method assigned automatically launches the Method Progress window (see 5.2.2). The Method execution window also includes a Multiple Pump Control toolbar with the following buttons: • Start: Starts the execution of the selected pumps and their Methods. See 5.2.1 for more details. • Pause: Pauses the execution of the selected pumps and their Methods. See 5.2.1 for more details. • Resume: Resumes the execution of the selected pumps and their Methods.
5.2. Method Execution Control 5.2.1. Starting, pausing, resuming and stopping methods When the execution task is entered (by pressing the Execute Methods button on the experimentation assistant toolbar), all methods are stopped and the information displayed is the same as when the execution task was last closed. As explained previously, there are start, pause, and stop buttons located on both the toolbar of the Method Execution window and the Method Progress that can be used to control the method.
5.2.2. Runtime execution information Whenever a set of methods is being executed on a group of pumps, Adagio will manage the communications to: • • • • Send the appropriate commands to each pump depending on its model. Set the real flow to each pump depending on the step sequence of the associated method (see 4.2.4). Detect the special conditions (stalling, errors, etc.) of each pump. Determine the current flow of each pump.
5.2.3. Controlling execution special situations during the Method The following table shows the events that are considered by the application in order to detect specific situations and the reaction it will have against them: Event Situation Reaction User presses “Pause” button Paused Method is paused (see 5.2.1) Pump answers “stalled” Stalled Method is paused, User is warned and given the possibility to resume / stop.
The flow evolution graph shows the evolution of the real flow along the time combined with the expected flow set during the method edit task. However, the following functionalities differ from the flow evolution graph used during the method edit: • • • • • Steps cannot be added, removed, modified or selected. Step markers and step blocks are not shown. Contextual menu is not available. An automatic horizontal scroll function is provided to visually synchronize the graph and the current time.
5.3. Method Data Logging The Data Log button, located on the Method Progress window, provides you with the option of exporting the data resulting from the previously executed method. This button is only enabled for methods for which data has been generated, that is, only for stopped methods. When the Data Log button is pressed, a Save as dialog is provided to select the destination folder and file name for the exported data.
• Event record This data sheet includes an Event Record Table with the following columns: o Current time: real start time (within the 24 hours of the day) of the event o Event time: start time (within the method execution) of the event o Event description o Current flow rate: the flow rate of the method at that time o Total volume infused until that time (accumulated positive flows) o Total volume withdrawn until that time (accumulated negative flows) o Total volume disposed until that time (difference bet
5.3.2. Bitmap report A bitmap (BMP) file is generated including a screenshot of the pump flow evolution chart (see 5.2.4) exactly as it appears on the window (that is, with the same dimensions, zoom, axis and content). If the Method Progress graph is zoomed in after a run, you can zoom out to view the whole method by holding down the Control key and pressing the auto scroll button . 5.3.3.
6. Appendices 6.1.
