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<h1>
User manual
<span>optimise<b>:</b>ms</span>
</h1>
<p>An excellent resource to guide your first steps
<br />using the Optimise MS application for data collection
</p>
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<p>Optimise MS is a system for recording data including demographics, clinical events,
treatments and
tests in a fashion interoperable with
<a href="https://www.cdisc.org/">Clinical Data Interchange Standards Consortium (CDISC)</a>
standards for Multiple Sclerosis.
Optimise MS allows researchers to better monitor MS patients’ progress, record outcomes and
evaluate
treatments.
</p>
<p>Users can enter demographic, medical history, clinical event, visit,
test and treatment data.</p>
<p>Optimise MS can be used in various settings and you can choose to install it in offline mode
as a desktop application, useful when a network connection is not available enabled or in
online mode, installed on your IT department servers usable by a whole team simultaneously.
</p>
<p>This guide assumes that the Optimise MS system has been successfully configured as described
at <a href="/#getting-started">Getting started</a>. An administrator needs to be defined who
can control permissions for data access and securely provide users with login details. The
PC and login passwords should be kept securely.
</p>
<h1 id="ug-patientID">Patient identifiers</h1>
<p>A patient identifier is required when creating a new patient in Optimise MS. The term Patient
ID, used in this guide, refers to this identifier which may correspond to the patient's NHS
ID, CHI ID or otherwise qualified hospital identifier. Optimise MS stores an independently
generated pseudo-anonymised ID along with the patient ID entered by the user at patient
creation time - this generated identifier is referred to as Optimise ID.
</p>
<p>The Optimise ID is included in the exported data (more about the export in the section <a
href="#ug-export">Exporting patient data</a>). Note that you can retrieve the original
patient ID using the <a href="ug-search">Search tool</a> by searching the corresponding
Optimise ID; you must be an administrator on the system to carry out this de-anonymisation
operation.
</p>
<h1 id="ug-login">Logging in</h1>
<div class="bs-callout bs-callout-info" id="onlineVersion">
<h4>For users of the online version</h4>
<p>To start using Optimise MS, first open your favourite modern
<a href="/index.html#support">Browser</a>. Then, enter the hosting address in the
address bar <i>(You may need the assistance of your IT administrator)</i>.
</p>
</div>
<div class="bs-callout bs-callout-info" id="offlineVersion">
<h4>For users of the desktop version, working offline</h4>
<p>To begin, simply launch the Optimise MS program installed on your computer. It might
be found on the desktop <i>(You may need the assistance of your IT administrator)</i>
and features the following icon:</p>
</div>
<img src="/img/desktopLaunchIcon.png" width="30%" alt="launchIcon">
<img src="/img/desktopLaunch.png" alt="launch"><br />
<br />
<p>Once done, you should see the the following screen.</p>
<img src="/img/loginPage.png" alt="login">
<br />
<br />
<p>Enter the user name and password (in the boxes as shown below) that were given to you and
click the
Login button. The default username is
<em>admin</em> and the default password is
<em>admin</em>.
</p>
<img src="/img/credentials.png" alt="credentials">
<br />
<br />
<p>If the log-in is unsuccessful, you will get a message as shown below. Re-enter user
credentials and
click Login.</p>
<img src="/img/loginFail.png" alt="loginFail">
<br />
<br />
<p>If the log-in is successful, you should see the following screen.</p>
<img src="/img/homePage.png" alt="initial">
<br />
<br />
<h1 id="ug-search">Searching patients</h1>
<p>You can search the database using the user-friendly search tool available after successful
log-in.</p>
<img src="/img/searchTool.png" alt="searchTool">
<br />
<br />
<p>To search by patient ID, select Patient ID from the drop-down list labelled as 'Search by:'.
</p>
<img src="/img/searchBy.png" alt="searchBy">
<br />
<br />
<p>Click on the box labelled 'Containing'- this is below the 'Search by' list- and enter the
patient
ID you want to search for.</p>
<img src="/img/searchPatient.png" alt="searchBox">
<br />
<br />
<p>As you type in search value box ('Containing' box), the patients with ID that contain the
text you
entered will be shown in the area below the search box. Basic patient information for each
listed
ID is also shown. If no patients are listed, then there are no patients with that ID already
in the database. You can begin to enter data for a new patient, by entering the ID- please
see
the section
<a href="#ug-createPatient">Creating a new patient</a>.
</p>
<img src="/img/searchPatientResults.png" alt="searchResults">
<br />
<br />
<p>Data files generated by Optimise MS using the
<a href="#ug-export">Export option</a> do not include the
<a href="#ug-patientID">patient ID</a>. Should you wish to retrieve the Patient ID, you can
do so using the Search
tool. You will need to obtain the Optimise ID (labelled 'USUBJID' in the CDISC standard) and
search by 'Optimise ID' in the
drop-down list.
</p>
<p>Search by fields other than Patient ID and Optimise ID (generated Optimise ID) is also
available.
The example below refers to a search by country of origin with search value 'Canada'. The
search
results include two patients; patients with IDs Optimise1 and Optimise2.</p>
<img src="/img/searchCountry.png" alt="searchCountry">
<br />
<br />
<p>Choose from the list of patient IDs below the search box by clicking on the patient box. To
view
and/or enter data for patient with ID Optimise1, for example, click on the respective box
(highlighted).</p>
<img src="/img/searchPatientResultsBox.png" alt="searchPatientResultsBox">
<br />
<br />
<p>The timeline and a summary of the patient's Medical History will be available in the left
panel.
An overview that includes the patient profile, the primary MS diagnosis and other sections
is
available
in the right panel (see next screenshot). You may add, edit, or delete data for these
sections
as described in
<a href="#ug-enterPatientData">Entering patient data</a>.
</p>
<p>To exit the patient's (here, Optimise1) records and return to the Patient Search page where
you can
search and create patients, click on
<img src="/img/xButton.png" alt="examplePatientProfileClose"> which is located near the top
center of the page as shown below.
</p>
<img src="/img/examplePatientProfileClose.png" alt="examplePatientProfileClose">
<br />
<br />
<h1 id="ug-createPatient">Creating a new patient</h1>
<p>There are two ways to create a new patient in Optimise MS; by clicking directly on the button
'Add
a new patient' at the top of the page or by using the search tool.</p>
<img src="/img/newPatientButtons.png" alt="createPatientButtons">
<br />
<br />
<p>To create a new patient using the first way, click on Add a new patient. Enter the patient ID
in
the Patient ID input box in the new patient profile form in the right panel. The form
includes
the patient consent status. You need to set the consent status for patient data sharing to
Yes
or No at this stage.</p>
<img src="/img/newPatient2.png" alt="newpatient2">
<br />
<br />
<p>Complete the form (the option Unknown may be selected where appropriate), scroll down to the
end
of the form and click Submit to create the patient. To cancel the patient creation, click on
<img src="/img/xButton.png" alt="close"> at the top right corner of the screen.
</p>
<img src="/img/newPatientProfileSubmit.png" alt="newPatientProfileSubmit">
<br />
<br />
<p>A warning message will be shown if any of the fields are empty or unselected when you click
Submit.
All the fields in this form are required in order to add the patient to the system. If you
see
the following message, please ensure the new patient profile form is completed before
clicking
Submit. Please note that some field propose explicitly the value 'Unknown', it is an
acceptable value as long as it is selected from the list.
</p>
<img src="/img/newPatientProfileError.png" alt="newPatientErrorMessage">
<br />
<br />
<p>If the patient creation is successful, you should see the following page. Please note that a
few
fields are conditional on the patient profile (Pregnancy, for example, is conditional on
sex)
and may be unavailable to some patients.</p>
<img src="/img/newPatientProfile1.png" alt="newPatientAfterSubmit">
<br />
<br />
<p>At any point you can return to the patient search page by clicking on
<img src="/img/search.png" alt="searchMagnifier"> in the left panel (see below).
</p>
<img src="/img/searchMagnifier.png" alt="searchMagnifier">
<br />
<br />
<p>You may also return to the patient search page by clicking on
<img src="/img/xButton.png" alt="close"> near the top center of the screen highlighted
below.
</p>
<img src="/img/newPatientProfileClose.png" alt="newPatientClose">
<br />
<br />
<p>To create a new patient using the search tool, select Patient ID as the search field list and
enter
the patient ID in the search value box. If there are no patients with the entered ID (here,
'opt'),
you may create a new patient by clicking the button</p>
<img src="/img/createPatientButton.png" alt="createPatientSearch">
<br />
<br />
<img src="/img/newPatient1.png" alt="createNewPatientSearch">
<br />
<br />
<p>Once you click the Create button, you should fill the new patient profile form in the right
panel
as described above. The patient ID is shown at the top of the new patient profile form- this
is automatically filled.
</p>
<img src="/img/newPatientProfile.png" alt="newPatientProfile">
<br />
<br />
<h1 id="ug-patientConsent">Updating patient consent</h1>
<p>Optimise MS is intended to be used after consent is given by patients to hold their data
outside
of a hospital or clinic IT system. The clinical user of Optimise MS must indicate that
appropriate
consent has been given.</p>
<p>You may update the patient consent status at any time. Go to the main patient profile page
and use
the highlighted control in the right panel to update the status of patient consent.</p>
<p>If the current consent status is set to Yes, the text on the consent button will read as
follows:</p>
<img src="/img/withdrawConsentButton.png" alt="consentButton">
<br />
<br />
<p>For patient profiles currently not consenting, the consent button will look like</p>
<img src="/img/consentButton.png" alt="setConsent">
<br />
<br />
<img src="/img/patientConsent1.png" alt="setConsent">
<br />
<br />
<p>The current patient consent status is always visible on screen. Clicking the consent button
in the
right panel updates this label accordingly.</p>
<img src="/img/patientConsent2.png" alt="consentLabel">
<br />
<br />
<h1 id="ug-deletePatient">Deleting a patient</h1>
<p>Administrator users may need to remove a patient from the database (i.e. Right to be
forgotten).
To delete a patient click on 'Delete this patient' in the right panel. Please note this is
only
available to administrator users.</p>
<img src="/img/deletePatientButton.png" alt="deletePatientButton">
<br />
<br />
<img src="/img/deletePatient.png" alt="deletePatient">
<br />
<br />
<p>Click on YES, I AM SURE! to confirm the deletion or click
<img src="/img/xButtonDelete.png" alt="close"> at top right corner of the pop-up message box
to cancel.
</p>
<img src="/img/deletePatientWarning.png" alt="deletePatientMessage">
<br />
<br />
<h1 id="ug-enterPatientData">Entering patient data</h1>
<h2 id="ug-patientOverview">Patient overview</h2>
<p>The Profile section in the Overview panel contains the profile data entered during patient
creation.
To edit the Profile section, click the button
<img src="/img/editButton.png" alt="editProfileButton"> next to Profile. Click on
<img src="/img/pii.png" alt="pii"> to view the Patient Identifiable Information.
</p>
<img src="/img/patientProfileEditButton.png" alt="editProfileButton">
<br />
<br />
<p>Edit the Patient Demographics form as necessary and click Submit to save the changes or
<img src="/img/xButton.png" alt="close"> to return to the Overview panel.
</p>
<img src="/img/patientProfileEdit1.png" alt="editProfile1">
<br />
<br />
<p>The Primary MS Diagnosis section in the Overview panel contains the most recent diagnosis
data.
To edit
this or add more diagnoses, click
<img src="/img/editButton.png" alt="editProfileButton"> next to Primary MS Diagnosis.
</p>
<img src="/img/primaryDiagnosisEditButton.png" alt="editDiagnosisButton">
<br />
<br />
<p>A list of all prior MS diagnoses is shown in the right panel. Click on
<img src="/img/deleteEntry.png" alt="delete"> to delete the diagnosis entry. Click on
<img src="/img/editButton.png" alt="editProfileButton"> to edit that entry.
</p>
<img src="/img/primaryDiagnosis.png" alt="primaryDiagnosis">
<br />
<br />
<p>The form in the right panel below becomes available if you click
<img src="/img/editButton.png" alt="editProfileButton">. Complete the form as necessary and
click Confirm change to save or Cancel or
<img src="/img/xButton.png" alt="close"> to return to the Overview panel.
</p>
<img src="/img/primaryDiagnosisForm.png" alt="editDiagnosisForm">
<br />
<br />
<p>To add more primary MS diagnoses, click on</p>
<img src="/img/addDiagnosisButton.png" alt="addDiagnosisButton">
<br />
<br />
<img src="/img/addDiagnosisButton1.png" alt="addDiagnosisButton1">
<br />
<br />
<p>Enter the diagnosis date and select the diagnosis term. Click Submit to add the entry or
Cancel to
return to the diagnosis panel. Click
<img src="/img/xButton.png" alt="close"> to return to the Patient Overview.
</p>
<img src="/img/addDiagnosisForm.png" alt="diagnosisForm">
<br />
<br />
<p>To add or edit Pregnancy data, click on
<img src="/img/editButton.png" alt="pregnancyEdit">. The most recent Pregnancy record (by
pregnancy date) is listed in the Overview Panel.
</p>
<img src="/img/pregnancy1.png" alt="pregnancy">
<br />
<br />
<p>Click on </p>
<img src="/img/pregnancyButton.png" alt="pregnancy">
<br />
<br />
<p>in the right panel to record a pregnancy or click on
<img src="/img/deleteEntry.png" alt="delete"> or
<img src="/img/editButton.png" alt="editProfileButton"> to edit or delete existing entries,
respectively.
</p>
<img src="/img/pregnancy3.png" alt="pregnancyForm">
<br />
<br />
<p>Fill in the form. Untick
<img src="/img/ongoingPregnancy.png" alt="pregnancyForm"> to enter outcome date, outcome
term and MedDRA code. Click Submit to record the pregnancy or
Cancel to return to the list of Pregnancies. Click
<img src="/img/xButton.png" alt="close"> to return to the Patient Overview.
</p>
<img src="/img/pregnancyForm.png" alt="pregnancyForm">
<br />
<br />
<p>To enter Immunisation data, click on</p>
<img src="/img/addImmButton.png" alt="immunisation">
<br />
<br />
<img src="/img/immunisations1.png" alt="immunisation">
<br />
<br />
<p>Enter data in the highlighted form shown below. Click Submit to add the new immunisation or
Cancel.</p>
<img src="/img/immunisationsForm.png" alt="immunisationForm">
<br />
<br />
<p>The immunisation records are added to the Overview panel as shown below. To remove an
Immunisation
entry, click
<img src="/img/deleteEntry.png" alt="del"> next to that particular entry.
</p>
<img src="/img/immunisationDelete.png" alt="immunisationDelete">
<br />
<br />
<h2 id="ug-medicalHistory">Medical history</h2>
<p>The filtering tool in the Medical History Summary allows you to select which medical elements
are
included in this section. This is especially useful for patients with considerable amount of
recorded data. To include Treatments and Tests only, click on the respective buttons.</p>
<img src="/img/mhFilter.png" alt="medicalHistoryFilter">
<br />
<br />
<h3 id="ug-visit">Visit data</h3>
<p>Each clinical consultation is represented as a Visit in Optimise MS. A “Baseline Visit” would
usually refer to the first visit at the clinical site or consultant responsible for the
database.
</p>
<p>Click on
<img src="/img/newVisitButton.png" alt="newVisit"> to create a new visit for the patient.
</p>
<img src="/img/newVisit.png" alt="newVisit">
<br />
<br />
<p>Complete the new visit form in the right panel. Select the reason of the visit from the list
of available
options- this includes Routine, Drug Monitoring, Relapse Assessment and Urgent. Click Submit
to create a visit.</p>
<img src="/img/newVisitForm.png" alt="newVisitForm">
<br />
<br />
<p>A warning message is shown if the form is incomplete when Submit is clicked.</p>
<img src="/img/newVisitFormError.png" alt="newVisitFormError">
<br />
<br />
<p>If the visit is successfully created, it will be added to the Medical History Summary and to
the
Timeline. Baseline visits are labelled as such.</p>
<img src="/img/newVisitSubmit.png" alt="newVisitFormSubmit">
<br />
<br />
<p>The reason for the visit entered when the visit is created is used to label the visit entry
in the
Medical History Summary. A relapse assessment visit is shown below.</p>
<img src="/img/relapseVisit.png" alt="relapseVisit">
<br />
<br />
<p>Enter Physical Measures and Vital Signs data, if available, by clicking on the highlighed
button in the Medical History Summary. Fill in the right panel form. Click Save and then
click on <img src="/img/xButton.png" alt="close"> at the top right corner to return to the
Patient Overview. To cancel the data entry and return to the Overview without saving, click
on <img src="/img/xButton.png" alt="close">.</p>
<img src="/img/vitalSigns.png" alt="vital">
<br />
<br />
<p>The data will be added to the Medical History Summary in the appropriate section
(Physical Measures and Vital Signs, here).</p>
<img src="/img/vitalAdded.png" alt="vitalAdded">
<br />
<br />
<p>Symptoms and Signs are recorded only at a high level in the Optimise MS database in an
attempt to
maximise the efficiency of their recording in the clinic and thus encourage their
completeness.
Symptoms reported by the patient and Signs observed by the neurologist are recorded
separately.</p>
<p>Click on 'Edit symptoms data for this visit' or 'Edit signs data for this visit' buttons to
enter
Symptoms or Signs, respectively, elicited at the visit. For baseline visits, these will be
labelled
as 'First symptoms/signs indicating MS'. For non-baseline clinical visits, they will be
labelled
simply as Symptoms/Signs.</p>
<img src="/img/visitSS.png" alt="symptomsSigns">
<br />
<br />
<p>Enter any present symptoms by clicking on the buttons or selecting a value from the drop-down
lists
in the right panel form. For example, the neurologist might have observed fatigue for the
patient.
Scroll down to the end of the form and click Save. To exit the form and return to the
Patient
Overview, click
<img src="/img/xButton.png" alt="close"> at the top right corner. The form can be edited at
a later time.
</p>
<img src="/img/symptoms.png" alt="symptoms">
<br />
<br />
<p>The recorded symptoms are added to the Medical History Summary.</p>
<img src="/img/symptomsAdded.png" alt="symptomsAdded">
<br />
<br />
<p>Similarly, enter any signs by filling and saving the Signs form in the right panel. As an
example,
the patient might have shown evidence for cognitive dysfunction with impairment of memory
and
had reduced sensitivity to the colour red with the left eye.</p>
<img src="/img/signs.png" alt="signs">
<br />
<br />
<p>Any recorded signs are added to the relevant section in the Medical History Summary after
Save is
clicked.
</p>
<img src="/img/signsAdded.png" alt="signsAdded">
<br />
<br />
<p>You will have the options of entering any comorbid affect by clicking on 'Edit
comorbidities'. The comorbitity records management panel will appear in the right panel.
Optimise MS uses ICD11 for the classification.</p>
<img src="/img/comorbidities.png" alt="signs">
<br />
<br />
<p> When looking to reference an comorbitity a drop-down list of International Classification of
Diseases codings defined by the World Health Organization (ICD11, see
<a href="https://icd.who.int">https://icd.who.int</a>) is available.
<br /><br />By clicking on the field, a browsing tree will appear. It will display the
`code` and `name` of the diseases.
Click on the arrows
<img src="/img/arrow.png" alt="interruptionFormMeddraArrow"> next to each grouping term in
the list to follow the expanding tree of terms and identify the
specific disease coding of interest. Click on the term to select it. Any term at any
level
may be added as ICD11.
</p>
<img src="/img/icd11.png" alt="interruptionFormMeddra">
<br />
<br />
<p>Click on 'Edit performance measures data for this visit' to enter Performance Measures data.
</p>
<img src="/img/perfMeasures.png" alt="perfMeasures">
<br />
<br />
<p>The EDSS can be entered in two ways; the neurologist’s estimated EDSS or the calculated EDSS.
The
neurologist’s estimated EDSS score can be entered in the highlighted box in the right panel
form.
</p>
<img src="/img/estimatedEDSS.png" alt="estimatedEDSS">
<br />
<br />
<p>Only valid EDSS total scores (0 to 10 by 0.5 increment excluding 0.5) may be accepted in this
field.
Entering an invalid total EDSS, for example 100, will generate an error. Please use the dot
notation
for the decimal point, i.e. 4.5 is accepted while 4,5 is not.</p>
<img src="/img/edssError.png" alt="edssError">
<br />
<br />
<p>Click Save for this estimated EDSS to be recorded. In addition, or alternatively, the
functional
systems can be scored separately and the total EDSS can be calculated by clicking on Open
EDSS
Calculator. The estimated total EDSS entered as described above is carried over to this
calculator
only if the score is saved (by clicking the Save button).
</p>
<img src="/img/openCalc.png" alt="EDSScalculator">
<br />
<br />
<p>Select a score for each EDSS subcategory. Hover over a score button to see the respective
score description
highlighted on the right. The calculated total score will be shown in the score box labelled
Computed total score (automatically generated). Note that an Ambulation score is required
for
the functional scores to be saved. The saved estimated total is carried over to the score
box
labelled Estimated total score (by the clinician). You may update the estimated total here
as
well.
</p>
<p>Click Save to record the scores and then
<img src="/img/xButton.png" alt="close"> to exit the calculator. To exit Performance
Measures and return to the Patient Overview, click
on
<img src="/img/xButton.png" alt="close"> at the top right corner of the EDSS form.
</p>
<img src="/img/edssCalculator.png" alt="edssCalculator">
<br />
<br />
<p>The EDSS Total and EDSS Subscores will be listed under Performance Measures in the Medical
History
Summary. The text of the total scores (estimated and computed) is bold and pink.
</p>
<img src="/img/edssAdded.png" alt="edssAdded">
<br />
<br />
<p>Optimise MS supports the generation of a free-text visit report, called a Communication. This
can
be exported as a .txt file. You may also copy and paste the entered text directly in a
document
such as a clinic letter generated by other software.</p>
<p>Click on 'Edit or export the visit report' to edit or export a Communication for the visit.
</p>
<img src="/img/communication.png" alt="communication">
<br />
<br />
<p>Specific field data entered for the patient from a visit can be added automatically to the
Communication
by selecting the appropriate buttons above the text area.</p>
<img src="/img/communication1.png" alt="communicationReport">
<br />
<br />
<p>Click on the buttons to add the respective recorded data to the report. You may format the
text using
the available formatting tools. The report can be updated at a later time to include data
entered
after its creation.</p>
<img src="/img/communication2.png" alt="communicationReport">
<br />
<br />
<p>For Clinical Events, Tests and Treatments, the time period to cover can be specified using
the drop-down
list. The default behaviour is to include observations/records of the last month. Select a
different
option from the list and click Add to update the report accordingly. Click the Save or
Export
button or
<img src="/img/xButton.png" alt="close"> to return to the Patient Overview.
</p>
<img src="/img/communicationTime.png" alt="communicationTimePeriod">
<br />
<br />
<p>Treatment and clinical event information covering the entire patient medical history were
added to
the Communication below using the appropriate buttons and selecting the entire patient
history
in the time period drop-down list.</p>
<img src="/img/trtEvents.png" alt="communicationTimePeriodCETreatments">
<br />
<br />
<p>Click on
<img src="/img/editButton.png" alt="edit"> next to the visit entry to update the visit
properties.
</p>
<img src="/img/editVisit.png" alt="editVisit">
<br />
<br />
<p>To edit the visit date or the reason for the visit, click on </p>
<img src="/img/changeVisitProperties.png" alt="editVisit">
<br />
<br />
<p>and to remove a visit click on</p>
<img src="/img/deleteVisit.png" alt="deleteVisit">
<br />
<br />
<h3 id="ug-test">Test data</h3>
<p>Click on
<img src="/img/testButton.png" alt="newTest"> to create a record for a new test for the
patient.
</p>
<img src="/img/newTest.png" alt="newTest">
<br />
<br />
<p>Select the date of the test, the type of test (Lumbar Puncture is selected below) and click
Submit
to create the new test. Click
<img src="/img/xButton.png" alt="close"> to cancel and return to the Patient Overview.
</p>
<img src="/img/testForm.png" alt="testForm">
<br />
<br />
<p>If the test is successfully created, it will be added to the Medical History Summary in the
main
panel as shown below. The test is also shown on the Timeline (green symbol) above the
Medical
History Summary.</p>
<img src="/img/testAdded.png" alt="testFormAdded">
<br />
<br />
<p>Click on Results to enter further data for the test.</p>
<img src="/img/testResultsButton.png" alt="testResultsButton">
<br />
<br />
<p>Complete the form in the right panel and click Save to record the test results.</p>
<img src="/img/testResultsForm.png" alt="testResultsForm">
<br />
<br />
<p>Entering non-numeric input where this is invalid generates the following error message.
Correct and
click Save.</p>
<img src="/img/testResultsFormError.png" alt="testResultsFormError">
<br />
<br />
<p>At any point you can click
<img src="/img/xButton.png" alt="close"> to cancel the test data entry and return to the
Patient Overview.
</p>
<p>Laboratory tests refer to blood or CSF tests only, e.g. total WBC, bilirubin and specific
anti-body
titres. After entering test results for a given reporting date, scroll down to the end of
the
page and click Save. Click
<img src="/img/xButton.png" alt="close"> to return to the Patient Overview.
</p>
<img src="/img/labForm.png" alt="labForm">
<br />
<br />
<p>Entering non-numeric characters in the laboratory tests will generate the following error
message
as numeric input is expected.</p>
<img src="/img/labFormError.png" alt="labFormError">
<br />
<br />
<p>Currently, only data concerning the presence or absence of T1 Hypointense Lesions, number of
T2 Hyperintense
Lesions and gadolinium (Gd) contrast enhancing lesions and brain atrophy scan result can be
entered
into the Optimise MS database. Some of the available fields for an MRI test type are shown
below.</p>
<img src="/img/mriForm.png" alt="mriForm">
<br />
<br />
<p>The data input in the MRI form is also validated. Entering non-numeric characters in Number
of enlarging
lesions, for example, will generate the following error message.</p>
<img src="/img/mriFormError.png" alt="mriFormError">
<br />
<br />
<p>The Evoked Potential test section allows recording of the P100 Visual Evoked Potential
amplitude
and latency. Sensory Evoked Potentials (SEP) with stimulation in the limbs are recorded if
Abnormal.
Data validation is applied here as well- only numeric input is accepted in some fields.
</p>
<img src="/img/evokedPotentialForm.png" alt="evokedPotentialForm">
<br />
<br />
<h3 id="ug-treatment">Treatment data</h3>
<p>Click on
<img src="/img/trtButton.png" alt="newTreatment"> to enter treatment data.
</p>
<img src="/img/newTreatment.png" alt="newTreatment">
<br />
<br />
<p>Fill in the treatment form in the right panel. Click Submit to record the treatment or
<img src="/img/xButton.png" alt="close"> to cancel and return to the Patient Overview. A
warning message will be shown if required fields
are not filled.
</p>
<img src="/img/treatmentForm.png" alt="treatmentForm">
<br />
<br />
<p>Unticking the box
<img src="/img/ongoingTreatment.png" alt="treatmentEnd"> allows you to record a treatment
discontinuation by entering the treatment end date.
</p>
<img src="/img/treatmentEndDate.png" alt="treatmentEnd">
<br />
<br />
<p>Any new treatment recorded is added to the Medical History Summary and the Timeline (yellow
symbol)
as shown below.</p>
<img src="/img/treatmentAdded.png" alt="treatmentAdded">
<br />
<br />
<p>To record any interruptions to a treatment, click on Interruptions and then Add interruptions
in
the right panel.</p>
<img src="/img/interruptionButton.png" alt="interruptionButton">
<br />
<br />
<p>Enter the interruption start date, uncheck 'The interruption is ongoing' to enter the
interruption
end date, if known, and record the Reason for the Interruption from the drop-down menu.</p>
<img src="/img/interruptionForm.png" alt="interruptionForm">
<br />
<br />
<p>If the interruption is related to an adverse event, the next section for Adverse Events
should be
clicked open. A drop-down list of adverse events defined by the Medical Dictional for
Regulatory
Activities (MedDRA, see
<a href="https://www.meddra.org">https://www.meddra.org</a>) is available.<br />
Note, however,
that MedDRA codings are subject to license. If you have a license ans which to use it,
please go to the <a href="#ug-meddra">Manage MedDRA codings</a>
section of this manual which will guide you through the upload process.
<br /><br />By clicking on the field, a browsing tree will appear. It will display the
`code` and `name` of the adverse events.
Click on the arrows
<img src="/img/arrow.png" alt="interruptionFormMeddraArrow"> next to each grouping term in
the list to follow the expanding tree of terms and identify the
specific adverse event of interest. Click on the term to select it. Any term at any
level
may be added as MedDRA.
</p>
<img src="/img/meddra.png" alt="interruptionFormMeddra">
<br />
<br />
<p>Complete the form and click on Submit to add the interruption details. Click the Cancel
button or
on
<img src="/img/xButton.png" alt="close"> to exit the interruptions section and return to the
Patient Overview.
</p>
<h3 id="ug-clinicalEvent">Clinical event data</h3>
<p>Clinical Events allow entry of data concerning relapses and other clinically relevant changes
or
adverse events including infections, opportunistic infections, death and other SAE likely
related
to treatment or malignancies.</p>
<p>Click on
<img src="/img/eventButton.png" alt="newEvent"> to record a new clinical event.
</p>
<img src="/img/newEvent.png" alt="newEvent">
<br />
<br />
<p>Fill in the form in the right panel and click Submit to add the event or
<img src="/img/xButton.png" alt="close"> to exit without saving and return to the Patient
Overview.
</p>
<img src="/img/eventForm.png" alt="eventForm">
<br />
<br />
<p>The event will be added to the Medical History Summary and to the Timeline (red symbol). You
may
add Symptoms and/or Signs associated with the Clinical Event using the relevant buttons in
the
clinical event entry in Medical History Summary, a process similar to the one for Visits
described
above.
</p>
<img src="/img/eventAdded.png" alt="eventAdded">
<br />
<br />
<p>To further describe the clinical event click on Data.</p>
<img src="/img/eventDataButton.png" alt="eventDataButton">
<br />
<br />
<p>Select the functional systems affected by clicking on the buttons, fill in the rest of the
form as
necessary, click Save and then
<img src="/img/xButton.png" alt="close"> to exit. Click
<img src="/img/xButton.png" alt="close"> before clicking Save to cancel the data entry.
</p>
<img src="/img/eventData.png" alt="eventData">
<br />
<br />
<p>The data fields for Infections and Opportunistic Infections are shown below- see right panel
forms.
</p>
<img src="/img/infection.png" alt="infection">
<br />
<br />
<img src="/img/opportunisticInfection.png" alt="oppinfection">
<br />
<br />
<h3 id="ug-editMH">Editing medical history</h3>
<p>Test, medication and clinical event data can be edited at any time by clicking the
highlighted buttons
in the Medical History Summary and following the steps described above. Additionally, for
Clinical
Events, Symptoms and Signs can be edited.</p>
<img src="/img/editData.png" alt="editDataButtons">
<br />
<br />
<p>To edit data about concerning tests, treatments and clinical events such as dates or type or
to delete
these entries, click on
<img src="/img/editButton.png" alt="editIcon"> as shown below. Click on one of the buttons
in the right panel to edit or delete the entry.
The informative labels in the right panel will indicate which actions and modifications are
allowed.
</p>
<img src="/img/edit.png" alt="editIcons">
<br />
<br />
<h1 id="ug-timeline">Using the Timeline</h1>
<p>You may click on the coloured shapes or EDSS on the Timeline to access (view/edit) the
corresponding
entry in Medical History Summary. The computed total EDSS is plotted at the bottom part of
the
timeline. If the computed total EDSS is not available (i.e. the calculator was not used or
the
user chose not to save the calculated score), then the estimated EDSS is plotted.
</p>
<img src="/img/timeline.png" alt="timeline">
<br />
<br />
<p>Click on
<img src="/img/timelineIcon.png" alt="timelineIcon"> next to Timeline to maximise the
timeline. The horizontal end point (right) of the timeline
is the current date. The timeline covers the last month by default. Therefore, any data
recorded
during this period is shown. You may change this behaviour by reading the guide below the
graph.
</p>
<img src="/img/timeline1.png" alt="timelineExpand">
<br />
<br />
<p>Follow the instructions below the timeline to interact with it. Zooming in and zooming out as
well
as navigation to a specific time period are available. The timeline shows Treatments,
Visits,
Tests, Clinical Events (Relapses and Adverse Events) and EDSS using different colouring.</p>
<p>Zooming out allows the depiction of a larger part of the patient's Medical History. For
example,
the patient's medical history for the year 2017 is shown below.</p>
<img src="/img/timeline2.png" alt="timelineOneYear">
<br />
<br />
<p>Further zooming-out gives a graphical overview of the complete medical history.</p>
<img src="/img/timeline3.png" alt="timelineAll">
<br />
<br />
<p>The treatment bands (yellow colour) are overlaid with the treatment names and types.</p>
<img src="/img/timelineTreatment.png" alt="timelineTreatment">
<br />
<br />
<p>Treatment interruptions are clearly marked with vertical lines that cover the interruption
period
(from the interruption start date to the interruption end date).</p>
<img src="/img/timelineTreatment2.png" alt="timelineTreatmentInterruption">
<br />
<br />
<p>Relapses can be characterised as mild, moderate or severe. The size of the circle depicts
this information
with larger circles representing more severe relapses. Where this information is not
available,
relapses are shown as
<img src="/img/relapseSymbol.png" alt="relapseSymbolTimeline">.
</p>
<img src="/img/timelineRelapse.png" alt="timelineRelapse">
<br />
<br />
<p>A severe relapse that started on the 7th of August 2011 and ended on the same date is shown
below.
The circle size represents the severity level and the dashed line indicates the duration of
the
event.
</p>
<img src="/img/timelineRelapse1.png" alt="timelineRelapse1">
<br />
<br />
<p>An opportunistic infection (Adverse Event) that lasted one month is shown below.</p>
<img src="/img/timelineAE.png" alt="timelineAE">
<br />
<br />
<p>A line chart is used for the the recorded EDSS with the scores being represented as black
labelled
points (dots) on the graph.</p>
<img src="/img/timelineEDSS.png" alt="timelineEDSS">
<br />
<br />
<p>An EDSS of 2.5 recorded in 2010, an EDSS of 4 recorded in 2013 and an EDSS of 4 recorded in
2015
are shown below. The scores are connected.</p>
<img src="/img/timelineEDSS2.png" alt="timelineEDSS">
<br />
<br />
<p>Click
<img src="/img/xButton.png" alt="close"> at the top right corner to exit the Timeline window
and return to the Patient Overview.
</p>
<h1 id="ug-export">Exporting patient data</h1>
<p>Optimise MS currently supports the export of patient data in JSON and CSV files. This is
available
in the right panel on the Patient Search page.</p>
<img src="/img/exportAll.png" alt="exportAll">
<br />
<br />
<p>In order to export the database as JSON and CSV files, click on the export button
(highlighted) and
choose where to save the ZIP folder which you can then extract. You may want to change the
name
of this folder- the default is attachment.zip. Please note that any Patient Identifiable
Information
is excluded from the generated JSON and CSV files by default.</p>
<img src="/img/exportAllButton.png" alt="exportAllButton">
<br />
<br />
<p>The patient ID is not included in any of the export output files; the Optimise ID (an
pseudo-anonymised generated ID) replaces the patient ID as described in the section
<a href="#ug-patientID">Patient identifiers</a>. The column USUBJID (Unique Subject
Identifier) in the exported treatment
data CSV file stores Optimise ID.
</p>
<p>You can find the respective patient ID using the search tool as described in the section
<a href="#ug-search">Searching patients</a>.
</p>
<img src="/img/export.png" alt="export">
<br />
<br>
<p>The option to export part of the database becomes available if you start using the search
tool.</p>
<p>Click on</p>
<img src="/img/exportSearchButton.png" alt="exportSearchButton">
<br />
<br>
<p>in the right panel to export the data stored for the patients listed in the search results
area below
the search tool.</p>
<p>You may export data based on a search by fields such as ID and treatment. Here, for example,
only
the data for patients diagnosed with RRMS can be exported by clicking the appropriate Export
button in the right panel.
</p>
<img src="/img/exportSearch.png" alt="exportSearch">
<br />
<br>
<h1 id="ug-admin">Admin menu</h1>
<p>Each installation of Optimise MS should have an identified administrator who manages Optimise
MS.
The administrator can create and delete user accounts, view the action log, where all user
actions
are recorded, and read messages about the software (e.g. the Optimise MS software version)
by
accessing the Admin Menu.</p>
<p>The administrator can click on the button located in the left panel as shown below to access
the
Admin Menu. Note that this is only available to users with administrator rights.</p>
<img src="/img/adminMenuButton.png" alt="adminMenuButton">
<br />
<br />
<img src="/img/adminMenu.png" alt="adminMenu">
<br />
<br />
<p>The administrator can manage the users (create and delete user accounts) by accessing the
relevant
option (Manage users) in Admin menu. In order to update or delete a user account, click on
the
respective entry in the list of registered user accounts in the middle panel.</p>
<img src="/img/manageUsers1.png" alt="manageUsersEditDelete">
<br />
<br />
<p>To update the password for a particular user, select the user from the list (hover over and
click
on the user entry in the middle panel), fill in the User Information form as shown below and
click Submit. Click Cancel to cancel the update.</p>
<img src="/img/editUser.png" alt="editUser">
<br />
<br />
<p>To withdraw admin rights for admin users, click on the tool shown below.</p>
<img src="/img/updatePriv.png" alt="editPriv">
<br />
<br />
<p>To delete a user, select from the users list and click on Delete.</p>
<img src="/img/deleteUser.png" alt="deleteUser">
<br />
<br />
<p>A warning message will appear. Click
<img src="/img/xButton.png" alt="close"> to cancel the deletion or YES, I AM SURE! to
confirm the deletion.
</p>
<img src="/img/deleteUserWarning.png" alt="deleteUserWarningMessage">
<br />
<br />
<p>You may create a new user account by clicking on the Create a new user button.</p>
<img src="/img/manageUsersNew.png" alt="manageUsersNew">
<br />
<br />
<p>Fill in the highlighted form and click Submit.</p>
<img src="/img/newUser.png" alt="newUserForm">
<br />
<br />
<p>The following error message is shown if the submitted form is incomplete. Please complete all
fields
and re-submit.</p>
<img src="/img/newUserError.png" alt="newUserFormError">
<br />
<br />
<p>The action log shows a detailed description of all the actions performed by users.</p>
<img src="/img/actionLog.png" alt="actionLog">
<br />
<br />
<p>Information about the software is also available in the Admin Menu.</p>
<img src="/img/systemInfo.png" alt="newUserFormError">
<br />
<br />
<h1 id="ug-meddra">Managing MedDRA Codings (admin only)</h1>
<p>The initial installation does not come with MedDra coding, due to license reason. The
software comes with an opt-in upload of the MedDRA codes, after which users can select
desired code in clinical events. NB upload can only be done by admin.</p>
<p>In the Admin Menu, select "Manage MedDRA codings"; you will then see the following panel.</p>
<img src="/img/uploadMeddraOnlyMdhier.png" alt="uploadMeddraOnlyMdhier">
<p>Depending on your subscription to MedDRA and your preference of the granularity of the
codings that will be in the application, select the appropriate option. Mdhier.asc contains
all the terms higher than "Low-level terms" and llt.asc contains all the "Low-level terms"
(in MedDRA terminology).</p>
<img src="/img/uploadMeddraWithLlt.png" alt="uploadMeddraWithLlt">
<br />
<p>Select the appropriate files of the indicated name in the files provided by MedDRA and click
submit. The application will start to process the file. When you see the following message,
the upload is finished:</p>
<img src="/img/meddraUploadDone.png" alt="uploadMeddraWithLlt">
<p>When you get a new version of MedDRA, you can update the codings in the application by doing
the same steps. If some patients already have MedDRA coding data associated with them, it
will be indicated that it is an old coding. If you decide to edit the MedDRA for a patient,
you will only be able to select from the new codings:</p>
<img src="/img/meddraOldCodings.png" alt="uploadMeddraWithLlt">
<h1 id="ug-update">Updating the software (desktop only)</h1>
<p>Optimise MS Desktop application is provided with a built-in update mechanism. To check if an
update is available and to perform the installation you must log in as an administrator and
visit the "Updates" section.</p>
<p>There you will be able to consult the update status and will be prompted to install is
applicable.</p>
<img src="/img/updateDesktopApp.png" alt="updateDesktopApp">
<h1 id="ug-logout">Logging out</h1>
<p>To log out click on the logout button.</p>
<img src="/img/logoutButton.png" alt="logoutButton">
<br />
<br />
<p>This is located in the panel on the left of the page as shown below.</p>
<img src="/img/logout.png" alt="logout">
<br />
<br />
<br />
<br />
</div>
</div>
<div class="col-md-3" role="complementary">
<nav class="bs-docs-sidebar hidden-print hidden-sm hidden-xs affix-top">
<ul class="nav bs-docs-sidenav">
<li>
<a href="#ug-patientID">Patient identifiers</a>
</li>
<li>
<a href="#ug-login">Logging in</a>
</li>
<li>
<a href="#ug-search">Searching patients</a>
</li>
<li>
<a href="#ug-createPatient">Creating a new patient</a>
</li>
<li>
<a href="#ug-patientConsent">Updating patient consent</a>
</li>
<li>
<a href="#ug-deletePatient">Deleting a patient</a>
</li>
<li>
<a href="#ug-enterPatientData">Entering patient data</a>
<ul class="nav bs-docs-sidenav">
<li>
<a href="#ug-patientOverview">Patient overview</a>
</li>
<li>
<a href="#ug-medicalHistory">Medical history</a>
</li>
<li>
<a href="#ug-visit">Visit data</a>
</li>
<li>
<a href="#ug-test">Test data</a>
</li>
<li>
<a href="#ug-treatment">Treatment data</a>
</li>
<li>
<a href="#ug-clinicalEvent">Clinical event data</a>
</li>
<li>
<a href="#ug-editMH">Editing medical history</a>
</li>
</ul>
</li>
<li>
<a href="#ug-timeline">Using the timeline</a>
</li>
<li>
<a href="#ug-export">Exporting patient data</a>
</li>
<li>
<a href="#ug-admin">Admin menu</a>
</li>
<li>
<a href="#ug-meddra">Manage MedDRA codings</a>
</li>
<li>
<a href="#ug-update">Updating the software</a>
</li>
<li>
<a href="#ug-logout">Logging out</a>
</li>
</ul>
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