The MiTO Web application aims to serve as a platform for facilitated exchange of information about preclinical models of translational oncology under simultaneous protection of know-how. Model types covered by MiTO include genetically modified organisms irrespective of species and developmental stage, transplantation models, carcinogen-induced models, and spontaneous tumor models, with the possibility to record metastasis sites as well as intervention studies. Beside tumor models, MiTO serves for data exchange about animal lines and cell lines.
This manual aims to ensure optimum support in enabling the user to deal with the web application MiTO appropriately, i.e. to use all functions of the program including registration, login, role acquisition, entering models, editing models, searching models, as well as management of departments, groups, and models. A unique hallmark of MiTO is to provide user a tool to define individuals or groups of people who get access to distinct models. This allows exchange of data among researchers on network level.
MiTO offers numerous tools to enter data and to access data released by other scientists.
Of note, MiTO offers a system of detailed rights correlating with roles in MiTO that reflect a hierarchical structure of a department represented by a head of department, department assistant(s), and researcher(s). This right/role system serves as a help to protect know-how and intellectual property. Within a department announced in MiTO, the role of the “head of department” assigns the ultimate authority meaning that the head of department has the full competence to warrant access to model fact sheets for selected individuals only, groups of persons or the public.
MiTO is a flexible web application, which is applicable on all modern browsers and in all monitor sizes as of a screen diagonal of 4 inches. In the browser Google Chrome 37.0, Mozilla Firefox 33.0, Apple safari 7 and Internet Explorer 10 as well as newer versions of these browsers MiTO was tested. Use of unsupported systems can lead to faulty representations.
If MiTO notices that, the browser does not comply with the requirements or the browser is too old, MiTO displays an error message.
If problems arise upon use of MiTO despite fulfilling prerequisites, the MiTO administrators appreciate feedback from the user. MiTO considers every feedback and channels it into future developments.
Structure and use of this guide
This user guide consists of six chapters. This section is a part of the first chapter, which introduces the basic facts of MiTO including this guide.
The second chapter covers the common functions used by every user of MiTO. They are not dependent on the ownership of an account for MiTO. Therefore, the chapter will focus on the use of the search, the registration, the login and the help functions.
The third chapter attends the successfully registered user, focusing on the mode of handling the own account, the internal messaging system, connection with departments (employments), and recording of tumor models, animal lines and cell lines in MiTO.
The fourth chapter deals with all functions available for the department management. It comprises the administration of the department, the employees and the models.
The chapters 1-4 give descriptions and figures for user with common computers or laptops with screen diagonals of 14-22 Inch. On other screen sizes, the displayed content could differ from the explanations. MiTO automatically adapts the displayed content to the screen size. Thereby the screen shows more or less information.
Chapter 6 presents a summary with few additional overviews and references.
This user guide version 2.0 has been based on MiTO version 05.10.03.
General and public functions of MiTO
Clicking on the tab “Search” leads the user to the page with the search overview. There are two different areas for the search. On the one hand, there is a general search area (“General search”) with a single input field and a button. This mode searches for any entered term in all tumor models, animal lines, and cell lines in the database. On the other hand, there is a more specific search area (“Specific search”) with three navigation-cards to enter specific and more comprehensive searches for each of the model types in MiTO (Tumor model, animal line, cell line).
Compared to other navigation-pages, in the general search area, there is a text field and a button instead of the navigation cards, but the functionality is similar. If the user enters a search term and hits the button next to the text field, MiTO opens the page for the general search and triggers a search. Consequently, MiTO already displays search results in the opened page.
The user can enter a varied number of words, letters, numbers and characters into the search text fields. The search algorithm searches for all models containing the complete search term, but also searches for models consisting parts of the search term. Space divides the different parts. As a result, the number of matches with the search term and parts of search terms prioritizes the hits. Aiming for the most accurate search, the user should renounce on expletives (“the”, “and”, “if”...).
If a user searches for an expression including space, for example “skin epidermis”, the user should embed the expression into quotes. The quotes prevent the search algorithm to split the search term on the spaces. This tends to result in a faster search. It is also possible to combine both methods, with and without quotes, in one search term. For example, SCC “skin epidermis” will search for all models with “SCC” and/or “skin epidermis” but not for models with only “skin” or only “epidermis”.
In some parts of the search, especially in the advanced search, there are dropdown menus with which the user can select a single value. In this case, the search algorithm treats the selected value as if it is in quotes. Later in this guide is more explanation about this case.
Triggering the search without a search term, does not lead to a result.
The “Search in all models”-button, mentioned before, leads the user to the general search. The surface of the general search is similar to the specific search described below, and is divided into 4 sections.
The first section serves for the search inputs. If there is still a pre-existing input in the text field of the navigation page, this section will display the previous input too. Next to the text field for the search term is the button “search”. A click on this button or a hit on the RETURN key on the keyboard triggers the search in MiTO.
As long as the search algorithm runs, the search will show the “search”-button grayed. After a successful search, the search displays the results in a section beneath the control-bar and deposits them in the user session of MiTO. This implies that the user always sees the latest search results as long as the user visits the search page within a session. This includes the specific search, too.
Beneath the search input section, there is a control-bar with three buttons. The first button, “show all”, displays all visible models (The chapter “Responsibilities” explains why only subsets of models are visible). The second button “reset” cleans the search results and the search terms on the page and in the session. Like in almost every page in MiTO, a “back”-button is available. As the name of the button indicates, the button leads the user back to the previous page. If the user visits a site of MiTO directly via URL or a hyperlink from another website, the “back”-button does not appear.
The most important part of the search is the section beneath the control-bar comprised of three tabs with the search results for the different model types (tumor models, animal lines, cell lines). The first tab always shows the tumor model hits, the second the hits for animal lines, and the third the hits for the cell lines. The next subchapter explains the different searches in more detail. Of note, the search results are similar within all search modes.
At the end of the page, there is a second control-bar with another three usable buttons to navigate to the specific searches of the different model types.
The view with the search results is identical in the general search and the specific search as described in the next subchapter. The result view consists of a section with filters, which act independent from the search algorithm, and furthermore gives an overview about the number of results with and without filter, and finally the concrete search results.
The user can apply the filters on the search results under selection of one out of three conditions. Every filter has a checkbox and a name next to it. Both indicate the status. The filter presented first with an empty checkbox. This implies that the filter is not in use. The user can click the checkbox or the name to change the status. The first click on the filter will fill a check into the checkbox, the name will become green, and the name becomes changed with an additional “only” on the sentence. For the output of results, this means, that only models are visible anymore which comply with the filter condition. For example, if the user once clicks the first filter “reporter models”, the text of the filter will change to “only reporter models” and the results will only display models manipulated with reporter genes. A second click on the filter changes the color to red and replaces the check with a cross. The name of the filter now additionally gets a “not”. In this example, the search would apply the filter “only not reporter models” and consequently, the results would only show models without reporter genes.
Depending on the model type, there are different filter types available as described below.
Tumor model filter:
- “Reporter models”: Tumor models with animal- or cell lines containing reporter gene(s).
- “Recombinase models”: Tumor models with animal- or cell lines containing recombinanase gene(s).
- “Genetically modified organisms”: Tumor models with one or more genetically modified animal- or cell line(s).
- “Chemically induced models”: Tumor models with animal- or cell lines, which contain chemically induced genes and tumor models with interventions using a chemical treatment to induce tumorigenesis.
- “Physically induced models”: Tumor models with animal- or cell lines, which contain physically induced genes and tumor models with interventions using physical treatment to induce tumorigenesis.
- “Transplantation models”: Tumor models with one or more transplantations, either syngeneic or heterogeneic.
Animal line filter:
- “Reporter models”: Animal lines with reporter gene(s).
- “Recombinase models”: Animal lines with recombinase gene(s).
- “Genetically modified organisms”: Genetically modified animal line(s).
- “Chemically induced models”: Animal lines with chemically induced gene(s).
- “Physically induced models”: Animal lines with physically induced gene(s).
Cell line filter:
- “Reporter models”: Cell lines with reporter gene(s).
- "Recombinase models”: Cell lines with recombinase gene(s).
- “Genetically modified organisms”: Genetically modified cell line(s).
- “Chemically induced models”: Cell lines with chemically induced gene(s).
- "Physically induced models”: Cell lines with physically induced gene(s).
Next to the filter on the right side, the the search results are presented. Every search result displays different body of information depending on the model type.
Search result for tumor models:
Every hit of the result list contains the name of the respective tumor model and its description.
Search result for animal lines:
Every hit of the result list contains the so-called short name, which is a user-defined short form of the animal line’s name or its lab code. Beneath the short name, MiTO displays the full name of the animal line that should be given according to the international nomenclature. Next to the full name the species of the animal line is given.
Search results for cell lines:
The hits of the result list for cell lines contain information about short and full name. However, instead of the species, the search result gives the cell type of the line.
A simple click on one of the hits of the list opens the detailed fact sheet of the respective model. The subchapter below provides a more detailed description of the fact.
If the search results in more than ten hits, the result presents ten hits per page, each. At the end of each page, there are the indices for the different pages. The user can switch the page by clicking on one of those indices. The characters “<<” and “>>”directs the user to the previous or next page.
MiTO fixes every specific search to a specific model type and only presents results for this specific model type, i.e. tumor models, animal lines or cell lines. However, the search input section consists of two tabs.
The first tab with the inscription “Simple search” makes a search with free chosen entries and is identical to the general search, but is restricted to one model type, only.
The second tab “Advanced search” leads the user to a view, which allows a selective search. The default view gives the user three pre-created rows related to search criteria, but the user is able remove a variable number of rows, down to the first row. Alternatively, the user can add more rows. MiTO displays the search requests from top to bottom. To perform an own search, the user has to select the criteria for the search. This happens via the dropdown menu in the second column “Search in”. Depending on the model type, there are different search criteria available.
- Tumor model
- Animal line
- Animal line species
- Animal line phenotype peculiarities
- Cell line
- Cell line species
- Cell line morphology or classification
- Gene name
- Mutagenesis approach
- Regulatory element
- Regulatory element species
- Organ with expression of mutated gene
- Cell type with expression of mutated gene
- Inducibility of mutation
- Tumor entity
- Tumor entity cell type
- Tumor entity organ site
- Organ site of metastasis
- Intervention type
- Transplantation route
- Transplantation cell type
- Experimental line ontogenetic stage
- Associated researcher
- Associated organization
- Associated department
- Animal line full or short name
- Animal line species
- Animal line phenotype peculiarities
- Gene name
- Mutagenesis approach
- Regulatory element
- Regulatory element donor species
- Organ with expression of mutated gene
- Cell type with expression of mutated gene
- Inducibility of mutation
- Associated researcher
- Associated organization
- Associated department
- Cell line short or full name
- Cell line species
- Cell line morphology or classification
- Gene name
- Mutagenesis approach
- Regulatory element
- Regulatory element donor species
- Organ with expression of mutated gene
- Cell type with expression of mutated gene
- Inducibility of mutation
- Associated researcher
- Associated organization
- Associated department
Next to this dropdown menu, is a text field, which enables as soon as the user selects a value from the dropdown menu. The user can fill the first search term in this text field by the same rules as in the general search. Beside the text field is a “+”-button to add new rows below for selected search. In additional rows, there is also a “-”-button to remove the associated row again. Another new element integrated from second row onwards is a dropdown menuleft-hand side. This menu gives the four logical operators “and”, “or”, “and not”, and “or not”, whiche connect the different rows in the final search request. For example, usage of these operators helps a user to create following search request: “Animal line short name” + “B6” + “and” +”Tumor entity cell type” + “lung”. This search request triggers the search for all tumor models bases on B6 mice and tumor entities in lung cells. Thus, such a very specific search or highly advanced search delivers a small number of hits.
The user can start the search by using the “search”-button in the control-bar next to the “show all”-button.
Detail view (fact sheets)
Many sites in MiTO offer possibilities to switch to a view displaying the model details, i. e. a fact sheet of any model, although the outlay and content of the fact sheets differ dependent on the model type. Besides the possibility to open fact sheets within MiTO, for example through the click on a search result, there is also the possibility to open a distinct fact sheet directly by its URL. The user just needs to write down a matching URL for the model type and the model ID. For tumor models the link is “/MiTO/Tumor%20model/[ID]”, for animal lines it is “/MiTO/Animal%20line/[ID]” and for cell lines it is “/MiTO/Cell%20line/[ID]” (“[ID]”, whereby the authentic ID of the model has to be entered.
The following text elucidates the fact sheet control-bar with its different buttons and the three types of fact sheets.
Fact sheet control-bar
Depending on a user's role and corresponding rights, the user has access to a different number of buttons in the control-bar. Of note, not all of the following buttons are available for every user.
These buttons are visible for user authorized to delete the model. Usually, these are the primary investigator of the model, the responsible head of department, the responsible department assistant and the MiTO administrator. This button irreversibly deletes the model and all related references from the database.
These buttons are visible for user authorized to edit the model. Usually, these are the primary investigator of the model, the responsible head of department, the responsible department assistant and other individually authorized user. The button opens the edit view of the model. The sub-chapter “Manage models” gives more information about editing models.
This button is available for all registered user. A user can use this button to indicate a faulty or nonsensical model to the MiTO administrator, who is going to check the report and contact the scientist in charge for the model. Uninvolved user cannot see the report and the submitter keeps anonymous for any user.
“contact [PRIMARY INVESTIGATOR]”:
This button is available for all registered user. Consider, instead of “[PRIMARY INVESTIGATOR]”, in reality the name of the primary investigator labels the button. A click on the button leads the user to the messaging view. This view enables the user to send a message to the primary investigator. The next chapter’s sub-chapter “Messaging” describes more details about the messaging in MiTO. As a feature, this button automatically inserts the primary investigator as receiver of the message and sets the message title to “Question to”.
“mark as favorite”:
These buttons are available for all registered user. The user can use the buttons to mark models as favorites. The corresponding subchapter gives more information about favorites. If a model is already marked, the button changes the "mark" into "remove" and inverts the functionality.
Moreover, the button "back"-is again available for all users.
Fact sheet for a tumor model
The fact sheet displays on top the model name in the orange colored title row. Beneath, the first section summarizes fundamental information such as Id, Description and Keywords.
The next section shows the animal and cell lines involved in the tumor model. MiTO displays the experimental lines in separate cards with their short name or label, full name, underlying species and the ontogenetic stage of the respective organism.
Occasionally, an animal- or cell line is not available for the observing user. If this is the case, the user only sees the short name or label and a notice on the card. If the used line is visible, the user is able to switch directly to the fact sheet of the line of interest by clicking on the card.
The next section displays manipulations such as transplantations or diet regimens and tumor entities of the model such as squamous cell carcinoma, sarcoma, etc. Depending on the model, there are different fields filled with information and descriptions. The fact sheet only shows up with the fields containing entries.
The penultimate section contains various additional informations, starting with all references entered for the model. A user can open each reference with an inscribed link in another tab by clicking the link. Next to the references are the attached files that are only visible for registered user.
In the last section lists the contact data for exchange of information/models, starting with "Available at" showing information about the primary investigator and the related department. The fact sheet ends with the entry date and the date of last-modifications of the model.
Fact sheet for an animal line
The fact sheet displays on top the model name in the orange colored title row. Beneath, a picture of the line's species is shonwn on the left along with the general information like Id, short name and species as word on the right.
If given, the next section offers additional information about special technologies such as the manipulation of the animal line with recombinase genes or reporter genes.The other fields show mutations of the breeding pair, genetic background, backcross generation and synonyms.
The next section is only visible if the animal line had some mutations. If so, the fact sheet displays the mutations in a tabular form. Every row in the table refers to a single mutation declaring the mutation type, the mutated gene along with its original species, regulatory elements along with its donor species, gene activity, and expression pattern throughout different organs and cell types.
This section is followed by further non-obligatory information about phenotype, characteristics and additional information, which again is only displayed if entered.
The next two sections are similar to the fact sheet for a tumor model containing references, attached files and availability.
Of importance, finally the fact sheet displays all accessible tumor models, which use this animal line. The user can click them individually and switch to the corresponding tumor model.
Fact sheet for a cell line
The fact sheets for a cell line and an animal line are similar. On top, the full name is displayed in the orange title, too. Beneath, there is a picture of the species, the ID, the short name, the cell type, the species, special technologies, original source (organ or tissue) and the genetic background.
If given, the next section contains the mutations, here without information about the modification of the gene activity and the expression pattern.
This section is followed by a section of secondary information. The fact sheet displays dynamically only fields with deliveries. In principle, the entries could be information about cell morphology, coherent disease, sex of the donor organism, characteristics and additional information.
The remaining sections with references, attachment, availability and corresponding tumor models is similar in outlay to the fact sheet for an animal line.
The registration procedure for MiTO seems to be circumstantial, but the procedure is very important, protects the quality of MiTO and allows the secure entry of own models. The target audience of MiTO is personal from scientific institutions and their environment. Therefore, the MiTO administrators check every user for relationship to the target audience. Only personal of scientific environment will obtain MiTO accounts.
The registration starts for every user with a click on the link "register" right beneath the DKFZ Logo. The link opens the registration form.
First, the user has to choose an organization. If the organization is not available in the connected dropdown menu, the user can use the "add organization"-button to add a new organization. This button opens a dialog, where the user can enter the name and address of the organization. The dropdown menu automatically selects the new organization.
The next fields are exclusively for title, first name, last name, email and phone number similar to other registration forms. To make it easier for the MiTO administrator to identify a user, MiTO asks the user to give an official email from the user's organization. Generally, the administrator does not confirm registrations from public emails like Gmail or Yahoo. After the registration, the user is able to change the email.
The text fields are followed by a dropdown menu, which offers three options. Usage of this dropdown menu is an obligatory step to limit the visibility of the own contact data (phone and email). The user has the option to release the contact data to every user, every registered user or none of the user. Since MiTO contains an internal messaging system, it is per se not necessary to share the contact information.
Importantly, the user has to accept MiTO's Terms and Conditions. Clicking on the link "Terms & Conditions" l opens the text of terms and conditions in a new tab.
Having filled all text fields and accepted the terms and conditions, Mito offers the button "register”. This button triggers a mail to the email adress laid down in the registration form. This email helps to verify the user. The user just has to click the confirmation link in the mail within 72 hours. This click activates the MiTO administrator to check the authenticity of the user. After the authentification process, the administrator sends a mail to the user to communicate the result of the authentication and, if accepted, with login credentials. This takes up to 72 hours during regular labourtime.
The user should immediately change the password on receive going to the website https://www.dkfz.de/passwd/index.html .
A user with an activated account can login to MiTO by the "login"-link on the right beneath the DKFZ logo. The login requires a username and the related password.
For security reasons, Mito documents the delivered usernames to follow failed logins in the database. MiTO never documents successful logins or given passwords. If a user enters three times a wrong password, the login disables the text fields and the user has to re-open MiTO.
Another strategy to protect the user’s data, especially the password, is to store the user data in the Active Directory of the Deutsches Krebsforschungszentrum in Heidelberg (DKFZ) under severe security rules. Additionally, MiTO demands to change the password every 90 days by the user. This rule of password change makes it on the one hand intricate for the user but on the other hand, the user benefits from proven security standards in the DKFZ.
If a user forgets the own password, the user can contact the MiTO administrator, for example, by sending a mail to firstname.lastname@example.org, or alternatively, by using the contact form on the MiTO website. As a rule, the user finds the contact form in the footer or behind the card "contact" in the tab "Help". The user has to select the option "Password forgotten" from the dropdown menu and to enter the own username or the MiTO-related email in the text field beneath.
After the contact to the administrator, the MiTO administrator will answer the user via the email in the user's account. The user has to confirm the loose of the password and then the administrator will send the user a new temporary password. The user should change the new password as soon as possible on the website https://www.dkfz.de/passwd/index.html.
Every password expires after 90 days. If the password expires, the user cannot login to MiTO anymore. To avoid this scenario, the user receives a mail from the DKFZ password administration twenty-eight days and eight days before password expiry.To prevent password expiry, the user has to change the password on the website https://www.dkfz.de/passwd/index.html. This is also possible if the password has already expired.
A user can change the password unsolicited anytime on this website https://www.dkfz.de/passwd/index.html. The user just needs the own username and the password. To protect this page from automated attacks, every request for a new password will need at least 30 seconds.
MiTO wants to give all users a high level of support to avoid as much problems as possible by the use of MiTO. On different pages in MiTO references of help are given. In addition, the user can open the help via the Tab "Help" in the menu. The help feature contains cards with the following topics.
This is an abstract of frequently asked user questions along with the answers of the MiTO administrators. This help feature strongly depends on user input. Therefore, every user with problems or questions related to MiTO should use the contact form to report to the MiTO administrator. Without exception, all questions, criticism and suggestions are welcome.
This is the most important contact point for questions, criticism and suggestions to the MiTO administrator. The form on this page contains a dropdown menu for a choice of different contact reasons. Beneath the dropdown menu is a text field for the user to substantiate the request. If the user sends the request, MiTO administrators get the request and answer the request.
Here, the user finds the current document.
This page contains a tabular overview about the permissions for models in MiTO.
This page presents some videos with the most important MiTO functions.
The patch notes contain information about the actual and previous versions of MiTO.
This page contains the responsible persons and institutions behind MiTO.
Change password or forgotten password
This page includes information about the modes of change or restoration a password. This page includes important links for the password.
This page offers an overview of all frameworks used in MiTO including most important information such as author, license and version.
Terms & conditions
This page contains the Terms and Conditions of MiTO, which every user have to accept upon registration.
Functions for registered user
As soon as a user receives the own login data, login and use of many new functions are possible. Uponthe first login, the user has a new tab "Account". If the user has an affiliation, there are other accessible tabs like "Editable models".
Within the tab "Account", among others there is a navigation-card named "User account". A click on this card shows all related user information stored in MiTO. These include the usual information about username, title, first name, last name, email and phone number. Next, there is the configuration for an email notification as soon as the user receives a private message in MiTO. Finally, information gives advice, if the user shows the personal contact data to every other user, just registered user, or none of other user. On this page, it is also possible to edit or delete the own account.
To edit the personal account, the user has to click the Button "edit", beneath the account information. This makes the information fields editable. However, the user cannot edit the unique username. The MiTO administrator determines the username once during the registration process and later changes are not scheduled. While the text fields replace the other information, radio buttons for "yes" and "no" replace the mail notification, and a dropdown menu with three options replaces the display of contact data.
The user can pass the edited values to the database with the "edit"-Button or retract them with the "cancel"-Button. Both buttons switch the view back to the display of the values.
The deletion of a user account is simple but the user has to consider some details. The user can find the “delete”- button in the red colored area below the user information. The use of this button will delete irreversibly the account data both, in MiTO and the Active Directory of the DKFZ. If a user deletes the own account unintentional, the user has to create a new account.
In case the user had therole of a head of department in a department in MiTO and there is no other head of department in the same department, the user should transfer all own models to other departments or should appoint a new head of department.
To avoid the accidental use of the delete button, every deletion process is accompanied by a dialogue, which asks the user to confirm the deletion. In this dialogue, the user can confirm the deletion with the "delete account"-Button or alternatively, cancel the deletion with the "don´t delete "-Button.
Within the tab "Account", there is a section "Messages" with five different navigation-cards to create and read messages as explainded in the following subchapters.
The first navigation-card "Message" is responsible for the creation of internal messages. Two sections for the message and a control-bar divide the page behind the navigation-card. The first section lists the receiver of the message and contains two buttons to add single user, departments or groups as receiver.
The button "add user" opens a dialogue to define a single user as the receiver. The user can choose the receiver by entering the receiver's username into the text field or by selecting the receiver from a dropdown menu of all registered user. MiTO autocompletes every entered username or gives a suggestion of possible usernames. It is not possible to enter an unknown username. To search a MiTO user in the dropdown menu is not a simple act, and therefore it is facilitated by some filter options. It is possible to use filter for the dropdown menu by clicking the button "show filter". This button shows two additional dropdown menus, where the user can select an organization and a department. If the user changes the selected department, the dropdown menu with the user switches its available options, so it always only contains user from the selected department. If the user enters a username or selects a user, the receiving user can be approved by clicking on the "take user as recipient"-Button. Otherwise, the "cancel"-button closes the dialogue.
Add group or department
The user can use the first dropdown menu to select a single department and the second dropdown menu to select a single group. Consider, the dropdown menu only contains departments and groups’ whith the user as a member. (Accessible groups are defined by head of departments and department assistants and are explained later). It is only possible to select either a department or a group. The user can confirm the selection by clicking on the button "take user from department or group as recipient" or the user can abort the dialogue with the "cancel"-Button. If the user confirms the selection, the receiver list shows every other user in the department or group.
MiTO displays all receivers beneath the two buttons. The user can remove single receiver with a click on the "x" next to their name.
The second section of the message is the area for the message itself with a text field for a title and a text field for a text.
The control-bar includes three different buttons. The known “back”-button redirects the user to the previous page. The “go to contact administrator”-button leads the user to the contact form. Finally, the user can click the “send mail”-button to send the mail to the entered users. If the user clicks the “send mail”-button and the mail has a title and a text, MiTO shows a dialogue listing all receiver. The user should use this dialogue to make sure thecorrectness. If everything is fine, the user can submit the mail with the “send mail”-button in the dialogue, alternatively, the user can abrogate sending with the “cancel”-button.
Note: MiTO encrypts every message.
The "Inbox" collects all messages in a table with the state "Submitted". Every message has one out of three self-explanatory statuses: "Submitted", "Completed", or "Rejected". The table gives an overview of the type, the title, the status, the transmitter and the transmission date. In the last row, there are different buttons, depending on the message type, to handle the messages. If a user closes or rejects a message, this will change the respective status and the message disappears from the inbox. The next sub-chapter describes the different message types and the corresponding buttons.
MiTO contains a huge number of different message types to represent different tasks.
"Role change request"
MiTO uses the message type "Role change request" if a user wants to change the own role within a department. Those kinds of messages address people in charge, i.e. the head of departments or department assistants, where the requesting user wants to change the own role. Persons in charge have two buttons in their inbox to deal with the user request, one to accept ("accept"-button) and one to reject ("reject"-button).
"Department join request"
This message is a typical request to head of departments or department assistants. MiTO creates this message if a user submits a request for an affiliation in a MiTO department. This type of request always contains two buttons in the inbox. The "show request"-button opens a page with details and the "reject"-button declines the request. The chapter "Manage departments in MiTO" provides more information about this process.
"'Head of department' request"
MiTO creates a new message entitled "Head of department request" if a user creates a request for the role of the head of department. This request is similar to the previous “Join department request" but it addresses only the MiTO administrator.
"New department without 'Head of department'"
MiTO creates a message entitles “New department without “Head of department” if a user enters a department without a head of department. This is explained in more detail in the sub-chapter Manage own affiliations later in this chapter. This message is very special, because the buttons of this messages are only visible in the related user outbox. The inbox shows the message without buttons. The first button in the related user outbox "edit and submit request" opens a page where the user can check and change the entered email as well as the name of the head of department. After this, the user can send the mail again. The other button "remove request" deletes the request.
This request addresses the administrator and represents a user contact request.
"Tumor model approval request"
Before other users, who are not directly involved in model creation, can see a model in MiTO, a head of department or a department assistant in charge have to confirm the model. This user guide describes how to enter or to approve models in the respective sub-chapters in this and the next chapter. This message type entitled “Tumor model approval request” offers three buttons in the inbox. The first button “show tumor model” opens the fact sheet of the tumor model, the button “accept” confirms the model and the button “reject” rejects the model and closes the request.
"Animal line approval request"
This message type entitled “Animal line approval request” is similar to the previous type “Tumor model approval request” but for an animal line instead of a tumor model.
"Cell line approval request"
This message type entitled “Cell line approval request” is similar to the previous type “Tumor model approval request” but for a cell line instead of a tumor model.
"New user request"
The registration of a new user automatically creates a message entitled “New user request” to the administrator, who can use the inbox buttons “activate user” to activate the user in MiTO, or the “reject” button to reject the registration.
In the inbox, a user message is equipped with the button “details” to display the full text of the message, and the button "close" to close the message.
A click on the report button in the control-bar of a fact sheet creates this kind of message entitled “Report” to the administrator. The message has a “details”-button for the entire report text and a “close”-button to close the report.
MiTO creates this type of messages to inform the user. In the inbox, there is only a button “close” to close this message.
"Change of accessibility"
If a user changes the accessibility of an approved model, MiTO creates a message entitled "Change of accessibility" for all heads of a department or department assistants in charge. The contacted user can utilize the inbox button "show accessibility" to switch to the actual accessibilities of the model and the button "close" to close the message.
If a user enters a new link within the references of a model, the MiTO administrator receives a message entitled “Check reference” with the request to check the link. The inbox contains a button “show reference”, which displays the specific reference in a new page. Here, the administrator checks the link for phishing sites, viruses, Trojans or similar risks. MiTO only shows links in confirmed fact sheets. The message also has a “close”-button to close the message.
"Change of reference"
This message entitled “Change of reference” is similar to the previous one, but the change of a link triggers the request for confirmation of a new link. A deletion does not trigger this message.
The message entitled “Check attachment” is also similar to the “Check reference” message. MiTO creates the message if a user uploads an attachment to a model. Checked attachments are visible for registered user. The MiTO administrator has to check the attached file for virus, Trojans and similar risks. The “show attachment”-Button in the administrators’ inbox opens a page for this check. With the button “close”, the administrator can close the request.
This message type addresses the administrator. The message informs the admin about a deleted user account.
The user’s outbox is the opposite of the inbox and collects all messages sent along with the type of message, title, receiver, transmission date and status. Messages with the type "New department without "Head of department'" come up with buttons "edit and submit request" and "remove request" instead of the status.
The inbox archive collects all messages with the either related status, which is “Completed” or “Rejected”. The table with the messages shows the type, title, transmitter, transmission date and status.
The outbox archive collects all messages sent along with the status which is either “Completed” or “Rejected”. The table with the messages shows the type, title, receiver, transmission date and status.
Manage own affiliations
In order to enter a model to MiTO, the user needs an account and an affiliation to a department in MiTO. This is very important because MiTO dedicates Models always to single departments instead to individual users. A user can manage the own affiliations with the navigation-card "Affiliation" under the menu tab "Account".
This page shows all accepted and requested affiliations in MiTO. Each displayed affiliation consists of a title that starts with “Affiliation at” and the name of the department. If the affiliation is not yet confirmed, MiTO adds the notion „NOT YET CONFIRMED" to the title. Sometimes, there is a hint beneath the title to indicate if there are open requests for a new affiliation or a new role.
The next text in the affiliation item shows the organization assigned to the department and the requested role of the user. Every displayed affiliation ends with some control buttons. If the affiliation is not confirmed yet, there appears a button "cancel request" to stop the request. As soon as a head of department or department assistant confirms the affiliation, two new buttons show up and the button “cancel request” disappears. The user can make use of the "quit affiliation"-button to finish the affiliation item. This removes the user as author and/or primary investigator from all models in the assigned department. The user can click the second button “request role change” to request another role in the department.
There is nothing but two buttons in the control-bar at the first time a user opens the page “Affiliations”. One of them is the above-described “back”-button. The other button “add new affiliation” opens the “Add affiliation” page.
The “Add affiliation” page dynamically leads the user to a new affiliation. First, the user has to select an organization in the dropdown menu, like upon registration. If the relevant organization is not included in the dropdown menu, the user can click the button "add organization" and add a new organization to the dropdown menu. The dropdown menu thereafter automatically selects the new organization.
Instantly after the appropriate selection, a new dropdown menu appears. The user has to use the new dropdown menu to select a department. Like with the organization, there is also a button to record an additional not yet existing department.
The next step gives the user the possibility to choose a role. The page displays every role with a radio button and a short description. The user has to choose one out of three roles as described below.
Head of department
A user with this role has the highest rights within a department. The user is able to see all confirmed models, all requests, all employees, and all model accessibilities of the department. Finally, the head of department is the only person within a department who is in charge to delete the department and all its models.
MiTO introduces this role to relieve the head of department. Therefore, the department assistant has almost all rights from the head of department and receives all automatically created mails for the head of department. The only limitation to the department assistant is that this role does not authorize to delete the department or to remove the head of department from the department.
This is the role for any other member of a department. The researcher can record models for the department.
If the department already assigned a head of department or if the requesting user is the head of department, the user is able to transmit the request. In the former case, a request is send to the assigned head of department asking for confirmation the affiliation. The mode of confirmation of such a request by a head of department or department assistant is explained in this user guide in the subchapter "Manage affiliated user" in the next chapter. In the latter case, the MiTO administrator is informed, who confirms the affiliation.
If the department possesses no head of department yet and the user is not head of department, MiTO displays three new text fields. The user has to fill in the first name, the last name and an email of the assigned head of department. Only if these text fields are filled, the user can submit the form. The submission creates an email for the inscribed head of the department with the invitation to register in MiTO and to confirm the affiliation.
It is possible to change the role in an existing affiliation by means of the button “request role change”. A click on this button replaces the previous buttons by a dropdown menu and two new buttons. The user can make use of the dropdown menu to select a new role. The button “send request” creates a request for a new role and sends it to the head of department. The second button “do not change role” removes the dropdown menu and the buttons without a request and displays the original default condition.
As soon as a user has an affiliation, the person can record models and gets a new tab “Editable models” in the navigation menu. The new surface behind this tab contains two areas. The first area "model collections" shows the navigation-cards for the own models and the own favorites. The second area beneath contains navigation-cards for creation of new models. The following sub-chapter of this user guide describes all functions of these areas. Of note, some of the described contents or functions contain three dots (“...”) which indicates, that the content or function is equal for all model types. The differences are just depending on the context, the three dots could mean “tumor model”, “animal line”, or “cell line”.
Editable tumor models
The use of the card “Editable tumor models” opens a page listing all editable tumor models. “Own” means, all models, where a user is the assigned author, primary investigator, or the model has the status “waiting for approval” or “approved” where a user is registered with the role of head of department or department assistant in the assigned department. This also applies to “Editable animal lines” or “Editable cell lines”.
The displayed table serves some short information about the tumor model. There are columns for the model id, name of model, name of primary investigator, name of author, name of department, and the status of the tumor model. An authorized user can change the name of the tumor model directly within the table. The user just has to click on the name twice, change the name and click somewhere else. If the entered name is empty or if the name has more than 255 characters, MiTO will not change the original name.
Here, a click onto the Id of the model opens its fact sheet.
Beneath the table is a control-bar with four different buttons. If the user visits the page, the first two buttons are disabled and the user has to select a row to enable the buttons. The button “delete” tries to delete the marked model. The user has to confirm this action in a dialogue, to prevent undesired deletion. A user has not always the right to delete a specific model in the table. If the user tries to delete a model without authorization, MiTO does not delete the model and shows the hint “You are not authorized to delete this tumor model”, else, the hint “Successfully deleted” appears. The use of the button “edit” opens the edit view of the selected model. The user guide describes the editing feature in more detail later in this sub-chapter. The user can use the button “add new model” to open the edit view for a brand new tumor model. Finally, there is also a “back”-button.
Editable animal lines
This page is similar to the page “Editable tumor models” with respect to the table and the buttons, adapted here to animal lines instead of tumor models. The only differences are of course the list of animal lines in the table and the column for animal line short name and the additional column for the species of the animal line. The short name is editable in an identical manner as the name of the tumor model.
Editable cell lines
This view is similar to the view for animal lines but with cell lines instead.
The page of favorites contains a table with any kind of model. The user has to mark a model in its fact sheet as favorite prior to the display in the table of favorites. The table contains columns for model Ids with hyperlinks to the corresponding model, name or short name depending on the model type, primary investigator and department.
The control-bar of this page contains a “back”-button and a “remove from favorites”-button. The second button removes a marked model (marked row) from the favorites and reloads the table. However, this removal does not delete the model from the database, but just from the favorites.
Enter a model
The user can record new models with the “add new ...” buttons in the control-bars of the ”Own ...” pages or with the “Create new ...” navigation cards beneath the “Own ...” navigation cards in the navigation menu tab “Editable models”. If the user clicks on one of those buttons, MiTO will open the edit view for a new model. This user guide explains the different elements and functions of the edition view below. The edition view always shows an overview or an input-area, and a preview of the models fact sheet.
The overview is the entry point for the editing process. This page shows the state of the model, with information about lack of data and about recorded data. This page also gives the user the possibility to jump directly to defined parts of a model.
On the top of an overview is a section giving the state of the model. The state influences the accessibility and changeability of the model. A newly created model always starts with the state "blank". There are four different states for models as explained below.
If a user creates a new model, the first state is “blank”. This means, MiTO has not yet recorded the model in the database. The only user with access to this model is currently the author.. If the user closes the model, the user cannot access it again. As soon as the user saves any change on the model, the status changes to “draft”.
As soon as a model reaches this state, MiTO documents the model in the database. The model is only accessible and editable by the author and the primary investigator. It is not essential to fill in the mandatory fields at this state.
waiting for approval
If the author or primary investigator has filled all mandatory fields with information, submission of the model is possible and of course, needs confirmation. While waiting for approval, the head of department and department assistant(s) of the assigned department can access and edit the model.
After a head of department or department assistant has approved the model, the author loses the right to edit or to delete the model and a user cannot empty mandatory fields anymore. In addition, the accessibility rules define which user can access or edit the model.
Note: This user guide contains a better overview about the default permissions in the sub-chapter "Default permissions" of the last chapter.
As long as a model has the status "blank", a button "use other model as template" next to the status is available. This button gives the user the opportunity to reuse existing models as templates and to reduce the input time interval. A click on this button opens a table with all accessible models. The user is able to select a model from this table and needs to click the button "use selected ... as template" to take the selected model as template. It is also possible to reduce the number of presented models in the table by utilizing the search field above the table to filter the models, or alternativel the checkbox beneath the table to show favorites. The user can also click the „cancel“-Button to go back to the overview without using a template.
Depending on the model type, there are different control-cards beneath the status area. Every control-card shows a quantitative summary of the related information, additional information, as well as the state of progress. Without exception, all types of models have control-cards for “Responsibilities”, “Basic information”, “References”, and “Attachments”. The control-cards for “Experimental lines” and “Manipulations and tumor entities” are exclusive for tumor models, while the control-card for "Mutations" is available for animal lines and cell lines, only. Exept of the control-cards for responsibilities and basic information, all other control-cards have a number within brackets next to their title. This number shows the number of instances entered in the related information. For example, if there are three mutations in the animal line, the control-cards title shows up as “Mutations (3)”. In such control-cards, the information about entries always depends on the number of instances. A model without mutations also has no mandatory fields in “Mutations”. Below is some additional description of the different control-cards.
This control-cards relate to the responsibilities assigned to a model and beside the progress and mandatory field requirements, there is no further information on the control-card.
“Basic information” control-cards
This control-cards relate to the basic information about a model and beside the progress and mandatory field requirements, there is no further information on the control-card.
“Experimental lines” control-cards
These control-cards relate to the experimental lines, i. e. the animal lines and cell lines used in a tumor model. The number in the title indicates the number of lines used in total, while the control-card lists the single lines by their short name or label. As long as there are no lines assigned to the model, there is just a note “No lines entered for this model”.
“Manipulations and tumor entities” control-cards
There is no information in this control-card as long as there are no experimental lines entered. In case the information about the experimental lines is given, but not about manipulations or tumor entities, there is the hint “No manipulations or tumor entities entered for this model”. As soon as a user enters a manipulation or a tumor entity, the control-card shows the manipulation or tumor entity related to the used line.
These control-cards also show a hint (“No mutations entered for this model”) if there are no mutations given for the model so far. If the user enters a mutation, the control-card displays the gene and the related mutations. There is no restriction in the number of mutations.
The control-cards show a hint similar to the control-cards before (“No references entered for this model”). As soon as a user enters a reference, the control-card shows a shortened form of the citation and the source.
Finally, the control-card named “Attachments” works similar as the control-cards described before. It also has a hint “No attachments added to this model” for empty attachments. If a user enters an attachment, the hint will disappear and the control-card shows the file names of the attachments instead.
Beneath the control-cards, there is the control-bar with up to four buttons. The exact number of buttons depends on the status of the model and the rights of the user. If the editing user has the right to delete the model, the first button will be “delete”. For a final deletion of the model, an extra dialogue appears which asks the user to confirm the deletion. After the deletion, MiTO leads the user to the assigned overview of own models, except, if the model is an animal line or a cell line extracted from a tumor model. In such a case, MiTO opens the tumor model again.
The next button is either “go to fact sheet” or “switch to tumor model”. The control-bar contains the second version only if the user opens the model throu a tumor model. As long as a model has the state "blank", the buttons are disabled. If the status changes, MiTO enables the buttons so they can direct the user to the model's fact sheet or to the related tumor model.
Next in line is the button “send for approval”. Only if the user has filled all mandatory fields, the button is operative. In addition, the button only exists as long as the model has the status “draft”. If the user clicks this button, the status of the model changes to “send for approval” and the assigned head of department as well as the department assistant receive an email entitled “... approval request” for the model. The chapter “Manage departments in MiTO” provides more information about the request.
The last button is the “back” button.
Normally, there is a preview of the model beneath the control-bar. On wide screens or screens with high resolution, MiTO shows the preview next to the control-cards or the input area of the model. The preview shows the fact sheet in real-time while the user is changing the model.
If the user clicks on one of the control-cards in the overview, MiTO replaces the overview with a specific input-area depending on the card. For example, the control-card “Responsibilities” opens the input area “Responsibilities”. Each input area has an own control-bar replacing the control-bar from the overview. The user can utilize this control-bar to shuttlebetween the next input-area, the previous input-area and the overview, with or without saving the changes. MiTO labels the buttons with their target area. Below, this user guide explains the different input-areas in more detail. Consider, that the input-area “Experimental line” and “Manipulations and tumor entities” are exclusive for tumor models and the input-area for “Mutations” is only available in animal lines and cell lines.
From the perspective of security, this input-area is the most important of all, because entries in this input-area define who can read or edit the model. Therefore, only the head of department or the department assistant are able to edit the information given in this view as soon as the model has the status “waiting for approval” or “approved”. In addition, if the model has reached the status “approved”, every change of the responsibilities triggers a message informing the head of department and all department assistants.
The first configurable data in this input-area is the department assigned to the model. If the author or editing user only has a single department, MiTO automatically displays this department and the user does not need to change anything. Else, the user has to select a department from the dropdown menu presented.
The next row just displays the author.
The following row appears with a dropdown menu, which lists user, depending on the selected department. The user has to select one of thelisted persons as primary investigator of the model. Of note, the primary investigator and the author could be the same person. Per default, MiTO preselects the author.
Below the dropdown menus, a section serves for the definition of the accessibility of the model, with two text areas and a checkbox. The user can use this section to define very explicit, which user can read or edit beside the head of department, the department assistant, the author and the primary investigator.
If the model should be readable for all other MiTO user without restrictions, then the user should check the checkbox “Public/WWW (read only)”. If the user checks this checkbox, MiTO disables the first text area. Elsewise, this text area is usable to set the readability. Every user or member of a group, department or organization in the text area is able to read the model. If a user starts typing in the text area, MiTO presents the collectivity of user, groups, departments, and organizations. The user can choose one of them and MiTO fills the instance into the text area, the user can repeat a process unrestricted, meaning that the user can fill in as much persons, groups, departments, and organizations as desired. The user can remove at any time an instance by clicking the “x” next to the instance. Per default, MiTO already implemented into this text area the selected department from the dropdown menue above. A color code should help to differ between the Instances. A user is dyed in grey, a group in turquoise, a department in green and an organization in orange.
Finally, a text area serves the definition of access to editing features. The mechanics of both text areas are similar. However, here in this text area, the user can only give access to editing a model to individual user or groups. Consider, a user with editing access cannot change the responsibilities.
“Basic information” input-area
The basic information differs a lot between the different model types, so the user guide discribesin this section the individual areas for each model type.
The basic information for a tumor model starts with a text field for a name. The user should choose an appealing name with a direct relation to the tumor models content. The next text area should contain a short description of the tumor model.
Beneath, MiTO provides a text area for additional keywords. They are very important to optimize the MiTO search. If the user starts typing into the text area, MiTO immediately presents the user some possible keywords starting with the same alphabetic characters. The user can select one of the offers or just type in another keyword. After each keyword, the user has to press ENTER or type in a semicolon (“;”). This punctuation indicates the end of the keyword. The step exactly this way is important because a single keyword can consist of more than one word if necessary. The text area displays every keyword with a grey border and an “x” next to the last word inside the border. The user can click the “x” to remove a single keyword from the text area.
To characterize the animal line and the cell line below, more elaborated basic information is needed. This data represents the primary line data. The user should fill in as much information about the animal line as possible, although the user only has three mandatory text fields to fill with data, the first of which is a field for a short name. The short name represents an abbreviation of the animal line’s name. For example, this could be the lab name or lab code or a common designation. Of course, it is also possible to use the official name already here. The next mandatory field, labeled with “Full name”, is the official name according to the internationally accepted guidelines. The websites http://www.informatics.jax.org/, http://dels.nas.edu/global/ilar/Lab-Codes or http://www.ncbi.nlm.nih.gov/omim may be helpful for to support the user in finding the correct nomenclature. For example, the mice strain with the full name “B6.Ptf1atm1 (cre) HnakKrastm4Tyj” has the short names “B6.KRas+/-P48Cre+/-“ or “B6.KRas+/-Ptf1Cre+/-“ or “P48Cre.K-RasG12D” that can be found in literature.
Beneath the described text fields is an additional text area for further synonyms of known names of the animal line. This text area is similar to the keyword area in the tumor model sheet and each synonym is separately accepted with ENTER or typing semicolon, too.
The third mandatory field is a dropdown menu for the species of the animal line. The user has to select one of the species. If the desired species is not in the drop down menu, the user is able to make use of the button “add new species” to open a dialogue. It gives the possibility to enter a new species to MiTO. MiTO then automatically selects the newly added species in the corresponding dropdown menu.
Next, there are text fields and text areas to describe the genetics of the line more detailed. The user can enter relevant mutations of the parents, general genetic background and backcross generation.
The next two text areas are for the description of the phenotype and further characteristics of the animal line.
The last text area is an additional chance for the user to enter any other important information about the animal line, which is not covered by an other field.
For the cell line, MiTO collects similar basic information as for the animal line. Here, again short and full name for the cell line are requested first. The following websites give an excellent overview about the official naming of cell lines: https://www.dsmz.de/catalogues/catalogue-human-and-animal-cell-lines.html, http://www.jhsf.or.jp/bank/CellName.html, or http://clkb.ncibi.org/. In addition to the name fields, there is also a text area for synonyms.
Next is a section, which describes the cell line. Beside a mandatory field for a species, like in the animal line, there is also a mandatory field for the cell type. No other fields are mandatory. This section also asks for data about the genetic background and the origin of tissue or organ.
In the next section, user can enter information that is more detailed. It can be that some fieldas are not to complete for every kind of cell line. Text areas serve for the description of morphology/classification, characteristics, and related disease. In addition, it is possible to choose the sex of the donor.
The user can enter all other informative data into the last text area in the input-area of the basic information sheet.
“Experimental lines” input-area
The experimental lines represent the animal lines or cell lines underlying a single tumor model. Therefore, this page has two buttons (“add an animal line”, “add a cell line”) to implement the lines used to establish a tumor model. If a user clicks on one of the two buttons, MiTO displays a table with all lines of the resepctive type that can be used or with other words lines that are accessible to a distinct user. The user can search the table with the search box located above the table or by checking the favorite checkbox. It is also possible to combine both modes.
If a line of interest is not available in the table, probably no user entered the line in MiTO yet, it is possible to enter a new line with the “create new ...” button. The button opens the option for anew line of the user. When the user has completed the data input for the new line, the user can navigate back to the tumor model with the control-bar buttons referring to the line. With the buttons “send for approval” or “switch to tumor model”, MiTO sends the user back to the input-area of the experimental lines in the tumor model’s data sheet and displays already the newly implemented line as experimental line. If the user clicks the button “back” or “delete”, MiTO navigates the user back to the input-area for experimental lines of the tumor model but omitting the line as experimental line.
In case the line is available in the table, the user is able to select the line with a single click on the specific row. Once marked, the user can choose the line as experimental line with an additional click on the “use selected ...” button.
The experimental lines in the related input-area are displayed along with a minimum of two buttons to either remove or replace the experimental lines. Consider a removal automatically removes all connected data like manipulations and tumor entities of the respective tumor model. With the "replace line with another line" button, all data connected to the replacing line are kept in the tumor model data set.
In addition, every experimental line has up to two text fields. The first of which only appears if the tumor model contains more than one experimental line with the same short name, else there is only the short name displayed. Otherwise, the user has to write an alternative label for the experimental line in this text field. The second field is always available and beneath the name/label. The user can take this text field to define the ontogenetic stage or passage of the line described.
Besides, there are different special scenarios with presentation of additional buttons. The first scenario is that the accessibility of the line used is more restricted than the accessibility of the tumor model. If this happens, a link to the responsibility card of the line shows up in the affected experimental line. The link opens a new tab in the browser and the user can re-configure the responsibility. If the discrepancy is intended, other user without permissions to read the line just see the name/label in the fact sheet of the tumor model. It is not mandatory to have all experimental lines on the same responsibility/accessibility level as the tumor model.
Another scenario could be that a user assignes an experimental line to another department than the tumor model. Such a case could arise if a user makes use of another tumor model as template. The author has to verify that all experimental lines used in the template are assigned to the same department as the tumor model. In this case, MiTO presents a hint with the appearance of a button (“copy line to current department”) in order to copy the experimental line of interest to the same department as the tumor model. This procedure copies all data but the responsibilities. Of note, MiTO takes the responsibility data given for the tumor model.
The last scenario happens if the user takes a template with an unaccessible line. In this case, the user has to replace or delete this unknown line.
“Manipulations and tumor entities” input-area
It is only possible to enter manipulations or tumor entities if there is at least one experimental line implemented into the tumor model.
If there is at least one experimental line, the site will show up with three buttons, i. e. “add a transplantation”, “add an intervention”, and “add a tumor entity” to add additional new data to the tumor model. Each procedure is encircled by a blue line and contains several input fields as well as a remove button.
Of note, the user is able to change the order all procedures of the site. This element allows to depict a chronological flow and to record an experiment as a standard operating procedure. To do so, the user has to click somewhere within a procedure (the encircled area) and hold the key. This changes the mouse pointer to a grabbing hand, releases the process from its position, and minimizes the displayed process. The user is able now to pull the chosen process to an arbitrary position within the processes. The new place is marked in MiTO by an orange line. If the user releases the mouse key, the process will drop to the marked position.
The different types of procedures are as follows:
A donor and an acceptor characterize the transplantation procedure. The user has to select the donor and the acceptor in the related dropdown menu associated with the title of the transplantation procedure. The dropdown menus contain already the chosen experimental lines of interest. Consider, the dropdown for the acceptor only contains animal lines out of the implemented experimental lines. The only mandatory field in the transplantation sheet is the text field for the cell type of the transplanted material. If the donor is a cell line, MiTO automatically adds the cell type of that cell line, and the related text field disappears. The user can use the remaining fields to keep record of the quantity of the transplanted material, the transplantation route, the result of the transplantation, and a description.
The description of an intervention always relates to a single experimental line. Thus, the user has to select the line of interest in the dropdown menu of the title. Furthermore, out of many different types of interventions, the user has to select a single type in the drop down menu beneath the title, a step that is mandatory. Although the completion of the remaining text areas is facultative, the user should fill in data to describe the intervention in more detail. There are text areas for a description, dose/concentration, frequency, and result. Consider that some text areas are not expedient for all intervention types.
The tumor entity classifies a tumor and thus data is needed from at least one experimental line. The user selects the informative experimental line relevant to the tumor model from a dropdown menue ofthe title, too. In the dropdown menu are only animal lines to choose. In opposite to the other processes, the user has to enter the tumor entity such as squamous cell carcinoma, sarcoma, lymphoma, etc. The text fields for classification, cell type and tissue/ organ are optional. Additionall, it is possible to record metastasis sites by adding an unrestricted number of metastases to the tumor entity. The user can add metastases with the button “add a metastasis site” and remove the data with the button “remove this metastasis”. Each metastasis record has text fields for the affected organ or tissue and for an additional description.
This input-area collects all driver mutations of an animal line or cell line. The user can add an unrestricted number of mutations by means of the button “add mutation”. This data can be removed again with the button “remove this mutation”. Every mutation data set contains three mandatory fields. The first one is the donor organism of the mutated gene. The user has to select the species of interest from a dropdown menu. If the the species is not available in the dropdown list, there is a button “add species” to complement the dropdown menu. The next text field is dedicated to the name of the mutated gene. If the gene is not yet entered in MiTO, four radio buttons appear. The user can utilize the radio buttons for additional characterization of the gene as a reporter gene or a recombinase or none of these categories. The third mandatory field indicates the mutation type, which has to be selected from a dropdown menu by the user.
Data entry into the next fields is optional. Starting with a text field for the regulatory element driving a gene of interest, a dropdown menu for the donor species of the regulatory element, and finally a dropdown menu for the modification of the gene activity serve to characterize the outcome of the genotype.
Mutations characterize animal lines and cell lines. In MiTO, there is a difference in recording the mutations of animal lines as compared to cell lines. The user can relate expression pattern to the mutation profile of animal lines, only. Therefore, in the mutation card a button named “add site of expression” appears. Any mutation in an animal line can be linked with an unrestricted number of expression sites, thus describing the known expression pattern. Each expression site is removable with the button “remove this site of expression”. In addition, each expression site contains a text field for the record of the relevant organ or tissue, a text area for the cell types, and a text area for additional notes. The text area for cell types works similar to the text area for synonyms or keywords embedded in the basic information. The user has to separate the different cell types with ENTER or a semicolon.
The references are very important to connect MiTO with other information sources about a model. References are Publications, Papers and Database entries. A user can add an unrestricted number of references to a model. The user only has to click “add reference” to implement a new reference or “remove this reference” to remove a reference. A single reference contains a mandatory field for the citation or Id of the reference. Beneath this text field is another text field for the source of the reference, for example the database or the publisher. The third text field in a reference is dedicated to an URL to the reference. Consider the MiTO administrator has to check every URL before other users can use the link in the fact sheet.
Under tumor models, is an additional button “add references from experimental lines”. This button allows importing all references from the experimental lines used.
The last input-area of each model contains attachments. They are only visible for registered user in the assigned fact sheet. A user can upload files with up to 4 mb size and one of the formats “pdf”, “jpg”, “jpeg”, “tif”, or “png”. Every uploaded file contains a text field for the file name and a text area for a description. The user can remove an attachment from the model and the database with the button “remove attachment”. Consider, before another user can see the attachment, the MiTO administrators check the attachment and have to unlock it.
Below a short summary is given, describing the corresponding output-areas for each model type.
Responsibilities, Basic information, Experimental lines, Manipulations and tumor entities, References, Attachments
Responsibilities, Basic information, Mutations, References, Attachments
Responsibilities, Basic information, Mutations, References, Attachments
The different input-areas contain a lot of text fields or text areas without input restrictions. Nevertheless, the user must not enter copyright protected content, not even own quotations if the user does not have the corresponding copyright, for example a literally quotation from a published paper. Therefore, the user should always type information into the text fields and should not copy and paste. If a user reports a model with copyright-related content, the administrator deletes the model and contacts the primary investigator.
If a user has the right to edit a model, there are several ways to visit the edit page. The user can go to the “Own ...” area, select a model and click the “edit” button beneath the table. Alternatively, the user can visit a model’s fact sheet and use the "edit" button in the control-bar of the model of interest
Consider a user is not able to save approved models with empty mandatory fields.
In addition, of note, the responsibilities for an approved model are only editable by the head of department or the department assistant(s).
Manage departments in MiTO
As soon as a user has an affiliation as head of department or department assistant, the user obtains new rights and duties in MiTO and a new menu tab “Management” with navigation-cards for management processes. Below, this user guide describes those management processes.
Change model permissions
In the management area behind the management tab is a section “Permissions”, which shares three different navigation-cards with the user. Each navigation card stands for the permissions assigned to model type. The pages behind the navigation cards show tables for each department of the user and the assigned models of the respective type.
The tables are almost identical for the different model types. There is always a column for IDs, a column for the name, and further columns for the “Short name” in animal lines or cell lines, the primary investigator, the author, and a column giving an overview about all other people, groups, departments, and organizations with access to the model. If the model is public, there is only a note of “Public” in the last column. The user can change the data in the columns referring to the name and primary investigator directly in the table. The user has to click on the name in the row to replace the name with a text field. The user can change the name in the text field and save the change with a simple click elsewhere. If the user only clears the text field, MiTO will not change the previous name. If the user double-clicks on the primary investigator, MiTO replaces the primary investigator with a dropdown menu, which serves to select another affiliated user of the department as primary investigator, who is then assigned to the model.
A click on the ID of a model opens the edit view of the model in the actual window.
The head of department and the department assistant(s) need at any time the full control about the department's models, which are visible for other user. Therefore, they have to approve every model before its release in MiTO.
Every unapproved model is combined with a button "send for approval", which is arranged in its control-bar. The author or the primary investigator is able to use this button to release the model. The button triggers a message of the type "... approval request" to all head of departments and department assistant(s) of the assigned department and changes the status of the model to "waiting for approval".
A single head of department or a department assistant has to approve the model within the own inbox, in which there are three buttons in the last column of the row with the request. The user can click the first button "show ..." to open the fact sheet of the related model. From the fact sheet, the user can utilize the "edit" button to change some data in the model, if necessary.
If the user does not need to check the model or has already checked it, the user is directly able to click the button “accept” to approve the model or the button “reject” to reject the model. The first button changes the status of the model to "approved" and releases it for all user listed in the responsibility card. The second button changes the status back to “draft”. However, both buttons close the request.
Consider a model with the status “draft” is only visible for the author and the primary investigator, while a model with the status “waiting for approval” is also visible for these people.
As soon as a model reaches the status “waiting for approval” or “approved”, only the head of department or the department assistant(s) can still change the responsibilities. To prevent false changes, which make the model accessible for un-authorized people, there is a secure system put on changes. Therefore, the change automatically triggers a message of the type “Change of accessibility” to all other persons in charge of the model. Another head of department or department assistant(s) can use this message to check the change and to reverse it in case of a mistake. In the inbox, two buttons are available in the row of this message. The first button “show accessibility” opens the edit view of the model with the “Responsibilities” input-area opened. The second button “close” just closes the message. The message is visible and processable for all heads of department and department assistant(s) of the corresponding department but not for the person who had introduced the changes. Only one of the addressed people in charge has to close the message.
Manage affiliated user
The first section in the management area contains a navigation-card “Affiliated user”. This navigation-card opens a page with a table containing all affiliated user of the department(s), where the user is head of department or department assistant. The table contains columns for the name, the username, the email, the phone number, and the role of the listed affiliated user. Consider every row in the table reflects a single affiliation and not a single user. This implicates that affiliated user may occur double in the table if the user is in charge for multiple departments and in different departments.
Release affiliated user
It is possible for a head of department or department assistant to dissolve an affiliation with the button “release affiliated user”. The user just has to mark the row with the corresponding affiliation and click the button “release affiliated user”. A released affiliated user loses all not explicit in the accessibilities noticed accessibilities to the models of the department. In addition, every model with the user was author or primary investigator, is complemented with those persons in charge, i.e. with the head of department.
Consider a department assistant is never able to release the own assigned head of department.
Change role of affiliated user
The table with the affiliated user also gives the possibility to change an affiliated user’s role immediately. The user just has to double-click the role in the affiliated user’s row. This replaces the displayed role with a dropdown menu with the three different types of roles. The user just has to select the new role and click anywhere to confirm the change. However, the role only changes if the chosen action does not break the following rules:
- -> A user can never change the own role.
- -> A head of department can never lose the own role by this procedure.
If a user submits a request for an affiliation, the head of department and the department assistant(s) receive a message to approve the affiliation. The head of department or department assistant can find the message of the type “Department join request” in the own inbox.
The message contains two buttons. The “reject” button serves to reject the request and close the message. The second button “show request” opens another page with detailed information about the request. The addressed user is able to change the requested user role on this page. After the check, the user can confirm the affiliation with the button “confirm user” in the page's control-bar or can go back to the inbox with the button “back”.
In the management area, there is a navigation-card “Departments”, which opens a page with a listing of all departments where the user is head of department or department assistant. The table on the page presents the departments with columns for the department’s name, cost center, head of department, organization, and number of affiliated user. A click on the number of affiliated user opens the page of affiliated user mentioned before. In this case, the table of affiliated user only shows the affiliated user of a single department. The functions remain the same: The user is able to edit the name and the cost center with double-click on the corresponding field in the department table. The double-click replaces the name or cost center with a text field. The user can change the content of the text field but cannot empty the text field. A click outside the text field safes a valid change.
If the user is the head of department, the user is able to delete the department. Therefore, the user has to mark the department's row and to click the button “delete”. Then a security dialogue appears where the user has to confirm the deletion. Of note, if a user deletes a department, MiTO also deletes every model assigned to the department.
Next to the “Department” navigation-card, is the navigation-card “Groups”. The setup of a group shortens the creation time of mails or the settings of accessibilities of a model. A head of department or department assistant can create one or several group for all affiliated user of the own department. The groups are configurable with a various number of users. The user of a distinct group can participate in several other groups of different department. With other words, a group could present a sub-department, a cooperation network, or just persons sharing similar core interests in tumor models, animal lines or cell lines.
The group table contains the name of the group, its member and the related affiliations (department(s)).
A user can delete a group by marking the associated row and clicking on the button “delete”.
The implementation of a group needs some interaction. The user has to click the button “add group” to open a new group page. On this page, the user first has to select the department of the group from a dropdown menu with the own affiliated departments. If the user has just one affiliation, the page displays the department of this affiliation without a dropdown menu and hence, the user does not need to select a department. The next mandatory field is dedicated to the name of the group. The group is only visible within the department so the user should choose a name, which most of the affiliated user of the department know. The user can use the text area beneath the name to describe the group. For example, the user can write down restrictions, so other head of departments or department assistant(s) understand the intentions and interests of the group. The last field is a huge text area for the member of the group. A user can enter a member to the group by typing in the name of the user and selecting the user in the appearing suggestions. This step puts the selected user into the text area and the user can enter the next user. To remove the selected user from the text area, click the “x” next to the selected user's name in the text area. If the user types the name of an unknown user, MiTO does not save this unknown (unregistered) user in the group.
The control-bar of the page contains two buttons, the simple “back” button and the “save” button. The user can click the “save” to finalize the setup of the new group.
If the user wants to edit a group, the user has to select the row of the group and to click the button “edit group” in the control-bar of the group table. The edit view looks similar as the add view. The only difference is that the user is not able to change the department of an existing group. Furthermore, it is not possible to save a group without a name.
Use of statistics
The third section in the management area contains statistics about the model types available in the own department(s). The pages behind the “... statistics” navigation-cards are identical. They always contain two graphical diagrams referring separately to the threemodel types of the own department(s). The first diagram shows the number of models that are public compared to the total number of models. The second diagram shows the number of models in the different statuses. This gives a head of department or department assistant the possibility to see at a glance the number of approved models, how many of them wait for approval and how many are actually in creation. The last one is most important, because the head of department or department assistant do not have access to models in the state "draft".
Adaptation of MiTO to different screen sizes and mobile devices
MiTO runs on a huge range of different devices and screen sizes. The focus of the MiTO development was the common personal computer or the laptop. Such devices with screens of about 16-24 Inches offer the best user experience. Nevertheless, MiTO is not limited to such screens or even Browser sizes. The user can arbitrarily utilize devices with bigger or smaller screens without the need to configure anything. MiTO automatically identifies the size of the Browser used and adapts the displayed information to that size. However, MiTO gets hard to use with a minimum browser size of 4 inch. In addition, MiTO prompts the user of small devices like smartphones to use the landscape mode. The landscape mode means the user holds the smartphone in the diagonal.
Below are the most important differences between the different sizes of MiTO.
Consider all figures in the user guide above relate to normal screens of 16-24 Inches.
The edit pages differ a lot between different screen sizes. Understandably, a user with a most possible huge display has the best experience with entering of models. The optimum is a screen with 22 inches. Those screens displays the preview next to the edit form and all necessary fields of an empty page are visible without scrolling. The bigger the screen the less scrolling is necessary. A higher resolution of the display brings the same effects as bigger screens but reduces the size of the displayed data.
A user also could enter models on smaller screens. However MiTO has to hide the hints, has to show labels, and fields one below the other in order to save the space and to prevent too small input-fields. This forces a user to scroll a lot more. Therefore, the MiTO administrators advise against using the entry forms on smartphones.
MiTO uses many tables to show a manageable amount of information. They would need horizontal and diagonal scrolling on small screen. This is not a good usability, so all tables have different display modes depending on the screen size. MiTO automatically hides columns depending on the screen size, so only the horizontal scrolling should be necessary. It is important to know, that this does not remove the information from the table. If a user wants to see the hidden information, the user has to click in the first column of a row and MiTO will show the hidden information beneath the row. A second click hides the information again. Consider many first columns contain IDs with embedded hyperlinks. In this case, the user should not click on the hyperlink but elsewhere in the column.
Editable columns are not editable anymore on small screens.
Specific terms in MiTO
Some words in MiTO or this user guide are abstractions from reality or are derived from technical terms. The table below gives some explanations.
|Department||Department is a MiTO equivalent to a department, division, section, or similar group within an organization. Models in MiTO always are assigned to a department. It is not possible that a user can enter models without assignment to a department. The department should always represent the real department of a user to mimic the real possession of models.|
|Department assistant||A department assistant in MiTO is a user who owns the confidence of the head of department and who assists the head of department with the management in MiTO.|
|Affiliation/ Affiliated user||An affiliation in MiTO is the association of a user with a department. This could, but do not have to, be a real employment. Affiliated user (employees) within MiTO and this user guide are always abstract terms and have nothing to do with payroll or similar.|
|Group||A group in MiTO is a user-defined group or configuration of user.|
|Head of department||A head of department in MiTO is the responsible person for a department in MiTO and in charge of all models in the department. A head of department in MiTO should also be a head of department in reality.|
|Researcher||Every affiliated user (employee) of a department in MiTO, who is not head of department or department assistant, is a researcher. The MiTO scientist does not need to be scientific personal at all.|
|(MiTO) Administrator||Administrator is technical and administrative personnel in charge of MiTO.|
|Navigation-card||The navigation-cards are clickable icons with a picture and a blue colored area with the card's name. On small screens, there is no picture on the navigation-cards. If a user clicks on a navigation-card, MiTO opens the corresponding page of MiTO.|
|Model types||The three different types of models in MiTO are tumor models, animal lines and cell lines. In the lettering of some buttons, there will be “…” instead of one of the mentioned types.|
|Navigation-area||The navigation-area is the area or page in MiTO with the navigation-cards. These navigation-areas always appear if the user clicks on one of the tabs in the menu of MiTO.|
Model state: Blank
Model state: Draft
Model state: Waiting for approval
Head of department**
Head of department**
Head of department**
|Head of department**
Model state: Approved
Head of department**
+++ optional +++
All user (Public/WWW)
Head of department**
+++ optional +++
Head of department**
|Head of department**
*= of the model
**= of the same department as the model
***= defined in the model