<p>Treatments are defined with two descriptors: the treatment used and the time period during which it was used. Treatments can be added, removed, edited, or created from scratch by clicking on the available buttons in the interface. Once treatments are added to the database, a dropdown menu will allow the selection of the specific treatment. The starting and ending times define when the treatment was performed, being the time relative to the manipulation of the limb (time 0). Zero is the default starting and ending time if no times are given. A treatment with negative time means that it was administered before performing the manipulation. When relevant, dosage information can be included in the title.</p>
                <p><img class="img-responsive center-block" title="Experiment treatments" src="/limbform/img/experimentTreatments.png" /></p>
                <p>A limb manipulation needs to be specified for the experiment. If no manipulation has been made, a wild type morphology can be selected as “no manipulation”. A previously defined manipulation can be selected from the dropdown menu, or a new one can be created. Clicking in the corresponding button, the manipulation editor can be opened from this screen in order to edit, copy, or create a new manipulation for the experiment (see <a href="#GroupManipulations">manipulations</a>).</p>
                <p><img class="img-responsive center-block" title="Experiment manipulation" src="/limbform/img/experimentManipulation.png" /></p>
            <div id="GroupExperimentResults" class="subgroup">
                <h3>Experiment results</h3>
                <p>The results of an experiment are specified with result sets. Each result set defines the outcome (resultant morphologies) for a given number of worms after a specific regeneration period since the manipulation. Result sets can be removed, copied, or created from scratch to describe the result of an experiment over different time periods or in different trials. If a different manipulation is used, a separate experiment must be made.</p>

                <p>Each result set contains several morphologies that correspond to the phenotypes observed in the experiment. Morphologies can be added or removed from the result set. A dropdown menu allows the selection of each phenotype, which can then be edited or copied, or a new morphology can be created from scratch (see morphologies). Finally, a frequency out of 1 for each morphology defines the penetrance of each of the morphologies in the specific result set. The sum of frequencies must add up to 1. If no frequencies are given, equal amounts are assumed.</p>

                <p>The following example shows the results from an experiment. Two different result sets were obtained. The first (result set A) specifies the resultant morphologies of 139 manipulated limbs after 3 days: 50% (69 limbs) regenerated the wild type morphology, whereas 25% (35 limbs) regenerated a lateral segment, and 25% (35 limbs) regenerated an intercalated limb. The second (result set B) specifies the resultant morphologies of another (or same than before) 19 limbs after 9 days: 63% (12 limbs) regenerated a double lateral segment, 21% (4 limbs) regenerated two separated lateral segments, and 16% (3 limbs) regenerated an intercalated limb:</p>
                <p><img class="img-responsive center-block" title="Experiment results" src="/limbform/img/experimentResults.png" /></p>
        <section id="GroupManipulations" class="group">
            <div id="GroupCreatingManipulations" class="subgroup">
                <h3>Creating manipulations</h3>
                <p>Before creating a manipulation, its category need to be selected in the category selector popup:</p>
                <p><img class="img-responsive center-block" title="Category selector" src="/limbform/img/selectCategory.png" /></p>
                <p>Manipulations are created and edited in the manipulation editor, which is divided into two panels. The left panel shows the graphical formalization (defined with a tree structure) of the manipulations being performed. The right panel shows a cartoon representation to aid in the visualization of the manipulation.</p>
                <p><img class="img-responsive center-block" title="Manipulation edit" src="/limbform/img/manipulationJoinFinal.png" /></p>
                <p>To add a manipulation action, left click on the previous manipulation action and then select the type of the new manipulation to add. A manipulation can be added between two existing actions by clicking the first one. Finally, a manipulation can be also deleted by selecting the appropriate action after right clicking on it:</p>
                <p><img class="img-responsive center-block" title="Manipulation menu" src="/limbform/img/manipulationMenu.png" /></p>
                <p>The type of manipulation actions are described below.</p>
            <div id="GroupManipulationMorphologies" class="subgroup">
                <h3>Manipulation morphologies</h3>
                <p>When starting a new manipulation, the first selection to be made is the morphology of the starting worm. Any existing morphology can be used or a new one may be created. To change the morphology, click on the morphology marker on the left half of the panel, and then select the desired morphology from the drop down menu on the right:</p>
                <p><img class="img-responsive center-block" title="Manipulation morphology" src="/limbform/img/manipulationMorphology.png" /></p>
            <div id="GroupPolygonalManipulations" class="subgroup">
                <h3>Polygonal manipulations</h3>
                <p>Three types of manipulations are defined by a single polygonal area: crop, remove, and irradiation. Selecting one of these manipulations actions will produce a box in the right pane. Drag the vertices of the box so that it covers the desired area. Left clicking then right clicking on a vertex will give the option to delete or add a vertex.</p>
                <p>Crop will keep only the area inside of the polygon:</p>
                <p><img class="img-responsive center-block" title="Crop manipulation" src="/limbform/img/manipulationCrop.png" /></p>
                <p>Remove will keep only area outside of the polygon:</p>
                <p><img class="img-responsive center-block" title="Remove manipulation" src="/limbform/img/manipulationRemov.png" /></p>
                <p>Relocate will crop the area inside of the polygon, and grafted into another place in the same limb:</p>
                <p><img class="img-responsive center-block" title="Relocate manipulation" src="/limbform/img/manipulationRelocate.png" /></p>
                <p>Irradiate represents irradiation within the polygon (the doses of the radiation are usually recorded in the manipulation name):</p>
                <p><img class="img-responsive center-block" title="Irradiation" src="/limbform/img/manipulationIrradiation.png" /></p>
            <div id="GroupJoinManipulations" class="subgroup">
                <h3>Join manipulations</h3>
                <p>The join manipulation action corresponds to grafting two limb parts together. Selecting a join action will produce a second branch in the manipulation tree. Here, a second morphology can be selected, along with any additional manipulation actions desired. The left tree represents the fixed piece; the right tree represents the movable piece. Once all desired manipulations have been added to the join tree, click on the join action marker in the left panel and both pieces will then appear in the right panel. Clicking and dragging inside the movable piece in the right panel will control the movement of the piece. Clicking and dragging outside the movable piece will control the rotation of the piece.</p>

                <p>The join manipulation bifurcates the manipulation tree, creating a left and a right branch with different actions:</p>
                <p><img class="img-responsive center-block" title="Join manipulation, left branch" src="/limbform/img/manipulationJoinLeft.png" /></p>
                <p><img class="img-responsive center-block" title="Join manipulation, right branch" src="/limbform/img/manipulationJoinRight.png" /></p>

                <p>The graft position and rotation is adjusted in the interface:</p>
                <p><img class="img-responsive center-block" title="Adjusting the join manipulation" src="/limbform/img/manipulationJoinRot.png" /></p>

                <p>The manipulation shows the final position of the two pieces grafted together:</p>
                <p><img class="img-responsive center-block" title="Join manipulation result" src="/limbform/img/manipulationJoinFinal.png" /></p>
        <section id="GroupMorphologies" class="group">
            <div id="GroupCreatingMorphologies" class="subgroup">
                <h3>Creating morphologies</h3>
                <p>Before creating a morphology, its category need to be selected in the category selector popup. A category restricts the type of segments that the morphology can contain.</p>
                <p><img class="img-responsive center-block" title="Category selector" src="/limbform/img/selectCategory.png" /></p>
                <p>Morphologies are created and edited in the morphology editor, which is divided into two panels. The left panel shows the graphical formalization of the morphology, while the right panel shows a cartoon representation to help with the visualization of the morphology being created.</p>
                <p><img class="img-responsive center-block" title="Morphology edit" src="/limbform/img/morphologyExample.png" /></p>
                <p>New morphologies are usually created by copying and editing the wild type morphology. However, new morphologies can be created from scratch as well.</p>
            <div id="GroupMorphologySegments" class="subgroup">
                <h3>Adding segments</h3>
                <p>The first step of creating a morphology is to define the segments it contains. Segments are defined as links between joints. To add a segment to an existing joint, right click on the joint and select the desired type of segment under “Add link”. In this example, we will add a new shank in the joint between the existing thigh and shank:</p>
                <p><img class="img-responsive center-block" title="Adding a new segment" src="/limbform/img/morphologyAddShank.png" /></p>
                <p>The resulting morphology will display the ectopic shank:</p>
                <p><img class="img-responsive center-block" title="Added a new segment" src="/limbform/img/morphologyAddShank.png" /></p>
                <p>Add region: adds a new region with a connection to the selected region.</p>
                <p><img class="img-responsive center-block" title="Add region and connect" src="/limbform/img/morphologyAddedShank.png" /></p>
                <p>In addition, a new segment can be added directly to an existing segment, without creating a joint between them. In this case, we right click on the segment and select the desired type of new segment under “Add link”. In the following example, we will add an ectopic foot segment in the existing shank segment:</p>
                <p><img class="img-responsive center-block" title="Adding a segment to another segment" src="/limbform/img/morphologyAddFootToShank.png" /></p>
                <p>The resulting morphology will display the ectopic foot:</p>
                <p><img class="img-responsive center-block" title="Added segment to another segment" src="/limbform/img/morphologyAddedFootToShank.png" /></p>
                <p>Apart from adding a new segment, right clicking on an existing segment will provide several other options:</p>
                <p>Change link type: changes the type of the selected segment. For example, the ectopic shank can be changed into an ectopic foot:</p>
                <p><img class="img-responsive center-block" title="Shank to foot" src="/limbform/img/morphologyChangeShankToFoot.png" /></p>
                <p>Resulting in:</p>
                <p><img class="img-responsive center-block" title="Shank changed to foot" src="/limbform/img/morphologyShankChangedToFoot.png" /></p>
                <p>Change link side: toggles between a left-side or right-side limb segment.</p>
                <p>Reverse: rotates the segment 180° with respect the proximal-distal axis.</p>
                <p>Invert: toggles the start and ending joints of the segment.</p>
                <p>Delete selection: deletes the selected segment.</p>
                <p>Any number of any types of segments may be added to the morphology in any combination.</p>
            <div id="GroupMorphologyAdjusting" class="subgroup">
                <h3>Adjusting joint and segment positions and sizes</h3>
                <p>Joints can be moved and resized to the desired place by clicking and dragging the marker in the left panel. The connected segments will change their size accordingly. For example, we can extend the length of the thigh by dragging its top joint:</p>
                <p><img class="img-responsive center-block" title="Change segment length and position" src="/limbform/img/morphologyChangeThighLength.png" /></p>
                <p>Every joint is defined by a number of external boundaries that defines the boundary shape of the limb. A joint connected to a single segment will have three external boundaries. A joint connected to two or more segments will have an external boundary between every set of connections. To adjust a boundary, left click and drag the red circle corresponding to the boundary.</p>
                <p>In the following example, we have reduced the size of the joint between the thigh and shank regions by dragging the red dots towards the joint:</p>
                <p><img class="img-responsive center-block" title="Change joint size" src="/limbform/img/morphologyChangeJointSize.png" /></p>
            <div id="GroupMorphologyDigits" class="subgroup">
                <h3>Adding digits and nerves</h3>
                <p>Digits and nerves can be added to the selected segment by right clicking the segment node in the left panel. To delete the selected digit or nerve, right click on its node in the left panel and choose “delete selection”.</p>
                <p>Adding a digit to a segment:</p>
                <p><img class="img-responsive center-block" title="Adding a digit to a segment" src="/limbform/img/morphologyAddDigit.png" /></p>
                <p>Resultant morphology:</p>
                <p><img class="img-responsive center-block" title="Added a digit to a segment, resultant morphology" src="/limbform/img/morphologyAddedDigit.png" /></p>
                <p>Nerves are defined by a list of locations defining the position of the nerve. To move the location of an organ, left click and drag its marker to the desired location. To rotate the selected organ, left click and drag the blue circle on the border of the marker.</p>
                <p>Nerves are defined by a list of points. Point can be added to a nerve to extend it. To adjust the location of the nerve points, select the nerve point marker, and then click and drag the marker.</p>
                <p>Adding the first point of a nerve:</p>
                <p><img class="img-responsive center-block" title="Adding the first point of a nerve" src="/limbform/img/morphologyAddNerve.png" /></p>
                <p>Resulting nerve point:</p>
                <p><img class="img-responsive center-block" title="Nerve point" src="/limbform/img/morphologyAddedNerve.png" /></p>
                <p>Adding a second point to the nerve:</p>
                <p><img class="img-responsive center-block" title="Add second nerve point" src="/limbform/img/morphologyAddNervePoint.png" /></p>
                <p>Resulting two-point nerve:</p>
                <p><img class="img-responsive center-block" title="Resulting two-point nerve" src="/limbform/img/morphologyAddedNervePoint.png" /></p>
                <p>Any number of nodes can be added to a nerve to define its path in the limb:</p>
                <p><img class="img-responsive center-block" title="Three-point nerve" src="/limbform/img/morphologyAddedNervePoints.png" /></p>
        <section id="GroupMisc" class="group">
            <div id="GroupMiscNaming" class="subgroup">
                <h3>Naming conventions</h3>
                <p>Any names may be used in the database, but several conventions were used when making the central database.</p>
                <p>The following rules were used for naming experiments in the database:</p>
                    <li>Experiments are named according to the first author’s last name, the year of the publication, and the number of the figure where it is described. Example: “Adell 2009 Fig. 2A”</li>
                    <li>If more than one publication of the same author and same year already existed, they were additionally labeled with a letter marker. Example: “Tasaki 2011b 3B”</li>
                    <li>Additional markers for figure number were used if more than one experiment came from the same figure, such as data from tables, that are labeled with a row and column designation. Example: “Oviedo 2010 Fig. 4A, 1-2”</li>
                    <li>If the experiment came from the text with no reference to a figure, the experiment was labeled with “text” and the page number. Example: “Beane 2011 Text p. 81”</li>
                    <li>If additional information that could not fit within the parameters of the experiment is essential (such as concentrations), it is given at the end of the experiment name, in parenthesis. Example: “Evans 2011 Fig. 5U, 1 (.5ug/ul)”</li>
                <h4>Manipulations and morphologies</h4>
                <p>Manipulations and Morphologies names are created as explicit and modular as possible. Manipulation names describe each type of manipulation action performed in succession. Morphology names describe sequentially each morphological variation from the wild type. The goal of using a modular approach is to aid in both locating existing entries and adding new entries in an organized fashion. Common traits are always put first in names, so that similar manipulations and morphologies are in close proximity in alphabetical order.</p>
                    <li>Example manipulation: “Amputation of femur (3rd instar)”</li>
                    <li>Example morphology: “Reverse palm, left limb”</li>
            <div id="GroupMiscZooming" class="subgroup">
                <p>Clicking off the image in either panel in an editor, and then holding ctrl and sliding the mouse wheel will zoom the contents of the screen in or out. Alternatively, when using a laptop pad, zooming can be achieved by holding one finger fixed and sliding a second finger.</p>
                <p><img class="img-responsive center-block" title="Zooming" src="/limbform/img/morphologyZoom.png" /></p>
            <div id="GroupMiscExporting" class="subgroup">
                <h3>Exporting images</h3>
                <p>Right clicking on the blank area of any image will give the option to export the image as a png, jpg, or bmp file:</p>
                <p><img class="img-responsive center-block" title="Exporting an image" src="/limbform/img/morphologySaveImage.png" /></p>