TAKAHASHI GROUP (情報化学研究室)

Hokkaido University

WEB APPLICATION FOR SEARCHING CHEMICAL ACTIONS AND NETWORKS

SCAN
User Manual
ENGLISH ORIGINALSCAN User Manual

HOKKAIDO UNIVERSITY - TAKAHASHI GROUP - INFORMATION CHEMISTRY LABORATORYSCAN User Manual
CONTRIBUTORSSCAN System Developers

Micke Nicander Kuwahara
Jun Fujima
This document was last updated
April 10, 2023 21:16
SCAN Web Application[Searching Chemical Actions and Networks]
Copyright © 2018 Keisuke Takahashi, Micke Nicander Kuwahara
in Takahashi Group (情報化学研究室) of Hokkaido University********************************************************************
SCAN is licensed under the GNU GPL License, Version 3.0;
you may not use this file except in compliance with the License.
You may obtain a copy of the License athttps://www.gnu.org/licenses/gpl-3.0.en.html
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions andlimitations under the License.
For any further information, visit the project GitHub athttps://github.com/scan-team/scan-platform-test********************************************************************
Takahashi Group
Hokkaido University, Faculty of Science, Department of Chemistry,
7th building, Room 7-510, Kita 10, Nishi 8, Kita-ku,
Sapporo, 060-0810, Japan.
scan-team@sci.hokudai.ac.jp
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SCAN User Manual

Table of Contents
CONTRIBUTORS.................................................................................................................1
Table of Contents..................................................................................................................................2
Preface..................................................................................................................................................3
Introduction..........................................................................................................................................4
SCAN Architecture..........................................................................................................................4
Web-based Browsing Interface........................................................................................................5
User's Manual.......................................................................................................................................6
SCAN Front Page............................................................................................................................7
SCAN Top Menu.............................................................................................................................7
Scan Front Page Footer....................................................................................................................7
Login and User Accounts.................................................................................................................8
Map Search Page.............................................................................................................................9
Map Detailed View........................................................................................................................11
Some Reaction Map Attributes.............................................................................................11
Map Nodes View............................................................................................................................13
Node Detailed View.......................................................................................................................13
Some Node Attributes..........................................................................................................14
Map Edges View............................................................................................................................15
Edge Detailed View ......................................................................................................................16
Some edge Attributes............................................................................................................17
Map Graph View............................................................................................................................17
Basic Interactions.............................................................................................................19
Advanced Interactions.....................................................................................................19
Node Selection............................................................................................................19
Shortest Path Selection...............................................................................................19
Deselect.......................................................................................................................20
Graph Drawing Modes....................................................................................................20
Available Graph Drawing Modes.........................................................................................21
Summary........................................................................................................................................23
Index...................................................................................................................................................24
Figure Index........................................................................................................................................25

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SCAN User Manual

Preface
A few words from the creators.

This manual is attempting to be a extensive guide to anyone who wishes to use the SCAN web
application found online at https://scan.sci.hokudai.ac.jp. The interactive chemical reaction
platform, SCAN, is developed for analyzing chemical reaction networks. SCAN offers thechemical reaction path network database, visualization, and network analysis tools. In
particular, SCAN is a web-based platform that allows users to perform interactive chemical reaction
path network visualization and data science techniques with simple operation. SCAN is designed toprovide a user-friendly graphic user interface, making preexisting knowledge of programming and skill
sets optional. Thus, SCAN is proposed to be an alternative tool for analyzing and understanding
chemical reaction networks.
SCAN is basically a visualization and analyzing tool for network data, with exclusive focus on chemical
reaction data. Currently there is no option for users to upload personal chemical reaction networks, butinstead the users are given the opportunity to load, view and analyze pre-loaded data maps that iscurrently provided to SCAN by the independant data-team who are cooperating with the SCAN dev
team. The data chosen and provided from the data team is a collection of AFIR data (Artificial Force
Induced Reaction), that is generated by a research group iCReDD at Hokkaido University lead byProfessor Satoshi Maeda. From a pure SCAN development team's point of view, there is no limitation onwhat type of data which could be loaded and analyzed in the application, but for the time being the data
team is only providing AFIR data.
So to be clear, the SCAN software development team is not involved in chosing and uploading thecurrently available data, and we do not take any responisbility for the data content. Our only focus is
the toolsets and the things one can do with the data or any data availabe on the site.
For any data related issues, please contact the iCReDD (https://www.icredd.hokudai.ac.jp) team at
Hokkaido University.
If you, when using our software, find any issues or come up with any suggestions for improvment, thatis related to the software itself, please feel free to contact us and let us know. SCAN is still a work inprogress and our goal is to make it user friendly and helpful for all chemical reserchers out there.

April 10, 2023
SCAN Software Project Leader
Director of Takahashi Group - Information Chemistry Laboratory

Professor Keisuke Takahashi
SCAN Software System Lead Developer

Micke Nicander Kuwahara

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Chapter

1

Introduction

Get to know what SCAN is and what it can do for you as a researcher and chemist.

Understanding the chemical reaction answers the fundamental mystery of how products areformed from reactants. First principle calculations unveil that the chemical reaction is acomplex matter as it involves a tremendous number of intermediates. In other words, achemical reaction can be treated as a form of a complex network consisting of numerous
molecular interactions. While it is difficult to capture the details of molecular interactions in anexperiment, first principle calculations play a major role in understanding such a complex reaction
map. In particular, numerous automatic chemical reaction searching tools have been developed such as
freezing string method with the Berny algorithm, single/double-ended growing string methods,
artificial force induced reaction (AFIR), reaction mechanism generator (RMG), and kinbot. Althoughsuch complex reaction networks become available, the question arises over how such complex networks
can be understood and how knowledge can be extracted, rendering tools for extracting the knowledge
from networks necessary.
Extracting knowledge from the chemical reaction network involves multiple steps and processes. In
particular, organization of chemical reaction database, statistical analysis, network visualization, andgraph theory are involved. Several network visualization tools are available such as Cytoscape andGephi which offer network visualization and graph theory analysis. Moreover, it has been demonstrated
that graph theory such as centrality analysis is found to be effective when determining intermediates.
However, these processes are strongly linked to each other, meaning that the individual development ofeach process could limit the ability to extract knowledge. In addition, network data visualization andanalysis often require particular skillsets as well as advanced programming skills, which can act asbarriers towards performing such analyses. Therefore, it is crucial to establish a centralized, interactive,
and user-friendly platform which has the ability to utilize these processes simultaneously. Here,
Searching Chemical Action and Network (SCAN) is introduced where a platform for interactive chemical
reaction network is designed and proposed where chemical reaction network producded by the AFIR
method. The SCAN platform is available at https://scan.sci.hokudai.ac.jp/ where it offers the users to
explore, visualize and analyze the chemical reaction network data generated by the first principle
calculation. Thus, SCAN offers the search and understand the complex chemical reaction network.

SCAN Architecture
The concept of SCAN is to store and share the chemical reaction network generated by the firstprinciple calculation where interactive network visualization and network analysis are also provided. Inorder to achieve the flexible reuse of data, the layered architecture consists of a data lake, data
warehouse, and data mart. Here, chemical reaction network generated by AFIR methods is used as aprototype chemical reaction network data where data is previously published. The chemical reaction
network data generated by AFIR contains numerous log files which are classified as raw data. These raw
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data are stored in their original form with no modifications. This data storage unit is defined as adata lake. The raw data provided by the data lake is then preprocessed for network visualization andnetwork analysis and stored in a data warehouse. Lastly, the data warehouse is accessed by the data
mart, which provides application services such as data visualization, data analysis, and an
application programming interface for data sharing.

Web-based Browsing Interface
Web applications are constructed where the three-layered architecture are used as the foundation. The
web application directly connects to the data mart, which allows the user to directly access the webgraphic user interface to carry out network visualization, network analysis, and data downloading
without previous experience with programming or data preprocessing. This is particularly attractive as
it expands access to chemical reaction analysis to researchers that may not have the knowledge orskillsets required for such research.

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Chapter2

User's Manual

So now you sit in front of your computer with the browser open and the SCAN website loaded inyour current tab. So now what? What should you do and how do you do it? Let's find out together,step by step.

In this chapter We will try to explain everything that you need to know about using SCAN in yourresearch and work, how to load data-maps, how you can study them in various way. How you can
open and analyze the node graph and find out more details about each node and edge of thechemical reaction data. Whether you will discover something new is more up to you though andnot the scope of this manual. We are software developers and not chemist, but by providing you withthis tool we hope that your trained eyes and extensive knowledge will help you perhaps see something
new that you have not seen before and take it from there. Let's teach you how to use this web tool to thefullest.

Figure 1: This is the first view that a SCAN visitor is met by
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SCAN Front Page
The first thing a SCAN Web application visitor sees is the SCAN Front Page as can be seen in Figure 1. At
the top is the top menu with its available options which will be present during the whole SCAN visit for
simple and quick navigation. Below that is the SCAN Logo and full application name. Below that is aquick access button to the reaction map search area just above some information about the currently
available amount of data stored in the SCAN Database. At the bottom of the page one can find a link to
the 'Terms of Use' page and a 'Contact Us'-link to the SCAN development team's mail address forsupport and other queries.

SCAN Top Menu
SCAN's top menu (as seen in Figure 2) is small and effective with basically only 4 choices, and inpracticality one could say there is only one real choice.

Figure 2: The Top Main Menu for the SCAN Web Application
The small SCAN logo to the left is a clickable link for returning to the original Start Front Page, Home soto speak. The 'Map Search' takes the user to the page where one can search for any of the available
reaction maps. 'Useful Links' is taking the user to a list of useful links and documents that might be ofuse. The last menu item, far to the right is the 'Login' (or if already logged in, the 'Logout') option.
It is required for the user to be logged in and have a proper SCAN account in order to access any of thedata and tools of the web application.

Scan Front Page Footer
At the bottom of the front page of SCAN, there is a small footer (as seen in Figure 3) with some useful
information and access point.

Figure 3: The footer links are only available at the first front page.
The 'Terms of Use' link will take the user to a page displaying all legal issues regarding the use of the
SCAN web application, while the 'Contact Us' link will open the user's associated mail-program and let
the user send a mail to the SCAN development team about whatever is on their mind.

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Login and User Accounts
When a user visits the SCAN web application for the first time, they need to create a SCAN account inorder to be let in any further. To do that one just clicks the 'Login' menu item at the top of theapplication which will then replace the current view with a Login/Sign Up view (as illustrated in Figure
4 below).

1. Figure 4: To the left is the Sign Up form, and for returning users
the Login form to the right will be used.
Creating an account is fast and easy, and the user will be immediately signed in after the creation has
been registered without any further hassle. It is important to use a valid mail address though, especiallyof one forgets the password and requests to be sent a mail to change it. Login for returning users isequally easy as can see in the figure above, with an option to bind the account to ones Google account if
so wanted. As soon as the login has been approved by the authentication system the user are promptly
returned to the front page of the SCAN Web Application, with the only difference that no the top rightcorner of the main menu says 'Logout' as a n option instead of previously 'Login' as can be seen below in
Figure 5.

Figure 5: If the user was previously and recently logged in, they will be
automatically logged in again.
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Map Search Page
It is on the Map Search page where the real fun begins and where one usually goes with speed after
loading the SCAN web application. The Map Search page basically contains of a small and simple searchform as can be seen below in Figure 6.

Figure 6: The Scan Map Search is the entry point for going further in to explore what SCAN has tooffer.
In the query filed the user can type any atom they are interested in and search to see if there are anymaps that contains that atom. After a short while after filling in the query filed and clicked 'Search' ,the result containing a list of reaction maps will appear below, as can be seen in Figure 7.
Each item in the list is a reaction map for a specific molecule, where the molecules chemical description
at the top, to the right, is the name of the reaction map and also the clickable link to get to that specificmap. Below are some other useful attributes that describes the map, such as internal database ID (goodfor exact reference), a list of containing atoms, the lowest energy value for one version of the molecule
as well as the highest energy value for another version. Also showing is the number of EQs, nodes in themap, meaning versions of the base molecule, and the number of TSs, edges or links, that is paths amolecule can take to transform into another version. Information when the map was created andupdated is also available at the end. To the left of the item block is an interactive 3D model of themolecule, that can be rotated and viewed by using the mouse inside the dedicated square.
If the result list is long, the user can sort and order the list based on any of the multiple available
attributes the map contains, in order to easier find the map they are looking for, as can be seen in
Figure 8.
The 'Switch View' button as can be seen at the top of each 3D molecule in e.g. Figure 7 can be clicked
and it will then change how the molecule is being displayed. The second view is still 3D, but have a bit
more colorful and 2D feel to it as can be noticed in Figure 9.

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Figure 7: The Search result showing the reaction maps that contains
the chosen atom.

Figure 8: The reaction map search result can be both sorted
and ordered based attributes.
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Figure 9: There are two types of views to use when looking at the
3D molecule.
When the user have decided which map they wish to look closer at, they click the blue molecule namelink, and will then be transported to the Reaction Map Detailed View Page.

Map Detailed View
After clicking on a specific map one is sent to a page showing all the available attributes that a map
contains. An example of such a map info page can be seen in Figure 10.
Below some of the more important ones of those attributes are described in more detail.

SOME REACTION MAP ATTRIBUTES
atom_name
These are all the names of the containing atoms.
natomsThis is the number of atoms present in the molecule.
lowest_energy
This is the lowest energy value present in the reaction map
highest_energy
This is the highest energy value present in the reaction map
neqThis is the number of nodes present in the reaction map, the numberof possible variants of the molecule. The value is clickable and willtake the user to a new page listing all nodes individually.

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nptThis is the number of edges (links) present in the reaction map, thenumber of possible paths to get from one molecule variant to another.
The value is clickable and will take the user to a new page listing alledges individually.
siml_temperature_kelvin
Which degrees of Kelvin were used for the different versions of themap

Figure 10: The full list of attributes that is contained
within each reaction map.
At the bottom of the attribute list there is a button that allows you to download the complete reaction
map as a CSV file, if you wish to study it in some other way and/or with some other tools.
At both the top and at the bottom there is also a clickable link that says 'Go to Graph Viewer', which if
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clicked will do just that for even more exciting ways to study the reaction map.

Map Nodes View
The Nodes List view Page, basically reached from the Map Details Page, contains of a list of every
molecule contained inside the reaction map. Each molecule is shown with a few key attributes and a 3D
visualization view-port that shows the specific molecule. An example of such list can be seen in Figure
11.

Figure 11: A list of all individual nodes in the reaction map
At the top of the screen is shown the name and id of the reaction map, and just above thenode/molecule list display, is an option to sort the list by energy instead of id number as can be seen in
Figure 12, as well as to chose how many to display per page.

Figure 12: The nodes list sorted by energy values instead
If any of the displayed molecule 'nodes' are clicked on its id link, the user is transported to view thatspecific molecule's detailed data.

Node Detailed View
After clicking on a specific molecule reaction map node, one is sent to a page showing all the available
attributes that the chosen molecule map node contains. An example of such a node info page can beseen in Figure 13.
There are 17 attributes shown on the site page, but all are not equally as important, so below is shown
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SCAN User Manualsome further detailed information only for those that are of more importance.

Figure 13: The detailed view of a specific molecule, reaction map
node, with all its data attributes.

SOME NODE ATTRIBUTES
Structure
This is a molecule 3D visualization for the map node, with an option toswitch display style as well as an option to download the xyz data forthe molecule to be used or shared externally.
Nid
Node Id, for easy identification.

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category
eq is the category identification for nodes
xyz
the xyz format that describes the molecule in 3D space.
energythe energy value for this molecule
gradient
the molecule gradient concentration
dipolethe molecule dipole moment value if present
hess_eigenvalue_au
The Hessian eigenvalue for this nodereactionyield
the yield amount this specific molecule is produced in a reaction.

Map Edges View
The Edge List view Page, basically reached from the Map Details Page, contains of a list of every
link/path from one molecule to another, contained inside the reaction map. Each link is shown with afew key attributes and a 3D visualization view-port that shows the specific molecules involved. An
example of such list can be seen in Figure 14.

Figure 14: The list of edges this reaction map contains.
At the top of the screen is shown the name and id of the reaction map, and just above theedge/link/path list display, is an option to sort the list by energy or connection instead of id number as.
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If any of the displayed 'edges' are clicked on its id link, the user is transported to view that specific edge
path's detailed data.

Edge Detailed View
After clicking on a specific molecule reaction map edge/link, one is sent to a page showing all theavailable attributes that the chosen molecule map edge contains. An example of such a edge info pagecan be seen in Figure 15.
There are 16 attributes shown on the site page, but all are not equally as important, so below is shown
some further detailed information only for those that are of more importance.

Figure 15: The detailed view of a specifc path, reaction map
edge, with all its data attributes.

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SOME EDGE ATTRIBUTES
Structure
This is a molecule 3D visualization for the map edge, with an option toswitch display style as well as an option to download the xyz data forthe molecule to be used or shared externally.
edge_id
Edge Id, for easy identification.
category
pt is the category identification for edges
xyz
the xyz format that describes the molecule in 3D space.
energythe energy value for this reaction path
gradient
the gradient concentration
dipolethe dipole moment value if present
hess_eigenvalue_au
The Hessian eigenvalue for this reaction pathconnection
connection0 and conection1 are the ids of the two nodes that this edge
connects.

Map Graph View
When one clicks on 'Go to GraphViewer' the view switches and a new interface is loaded below theapplication main menu, which contains of a simple upper sub menu, some instructions and buttons anda large drawing area where the reaction map data will be displayed as a network graph with nodes andlinks, representing all molecules and their transforming paths .
The default network is drawn immediately and it is weighted by the nodes energy values, where thehigher energy value (closer to 0) is of a more red (warm) color and lower (more negative) is of a more
blue (cold) color. An example of this view can be seen in Figure 16.

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Figure 16: The Reaction map displayed as a node graph with each molecule node and it'sconnections edges.
What one will quickly notice is that all the nodes and the whole map is shaking, quite violently. This isbecause the network graph is trying to adjust each node's position according to it base setting for
gravity and such between nodes. If one wish to wait for it to finish by itself, it might take quite a while,so therefore there is a green button that says 'STOP' at the top and which will hold the current position
for each node. In this state the user can manually move the nodes individually with drag and drop. The
green button then change to 'RESUME', which naturally allows the user to resume the auto location
correction feature to begin again if wanted. The Figure 17 shows this state.

Figure 17: After the auto adjusting of nodes have stopped, each can be manually moved.

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Basic Interactions
The base interaction a user can do with the network graph as a whole is to pan it by dragging the mousein the white area and zoom with the mouse wheel.

Figure 18: When hover the mouse above a node it shows the molecule 3D view which
the user can interact with.
In Figure 18 we can see how a popup window shows up as we hover above a specific node and show us
an interactive 3D view-port of that node's molecule. Using the mouse one can rotate the molecule freely
and with the 'Switch View' button the style of the molecule drawing changes.
If one double click on a node a new tab will open showing the selected node's detailed info page as
mentioned before and seen in Figure 13.
The color and size of a node is informative and relevant, but what it exactly means depend on whichmode the network graph is currently shown in, which will be further explained further on.

Advanced Interactions
How these interactions are done are also explained, in simple words, in the instructions above the
network graph for better help and support.
Node Selection

If one clicks on a node while holding the SHIFT-key, the node will be selected (grow in size and turnyellow). All neigbouring nodes connected to the selected node will also be semi selected (grow in size
and turn pink) for the user to easily track relationships. This can be seen in Figure 19.
Shortest Path Selection

If one instead clicks a node while holding the CTRL-key (or the mac-key on an Apple computer) one
initiate the process of calculating the shortest path between two nodes. The one clicked on will turnyellow and the system is now waiting for the user to CTRL-click yet another node. The user can thenpick any other node and click on it while holding the CTRL-key.
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Figure 19: A node and its neigbours selected.
As soon as that is done the system will then calculate the shortest path from the frist node to the final
node. Mark them all in pink colors and add a number to each node starting with 1 on the first clicked
node and then so forth. The user can now see the shortest path between two nodes, which other nodes
are involved and how many of them. An example of this can be seen in Figure 20

Figure 20: The shortest path between two nodes.
Deselect

To deselect all current selected nodes the user just needs to click the light blue button above the
network graph named 'RESET SELECTION', and then the graph goes back to default state and all ready tohave other nodes selected instead.

Graph Drawing Modes
To the left above the network graph is a drop down box that allows the user to change how the network
should be weighted and structured. The top-most default setting is 'Energy' which uses the reaction
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map's energy values is weights gor the network graph. As have already been shown in Figure 16 andFigure 17.
The other modes can be seen in Figure 21, and are further explained below. In Figure 22 one can see one
other example of such a different mode of calculating and drawing the network graph.

Figure 21: The different Graph drawing
modes available.

AVAILABLE GRAPH DRAWING MODES
Energythe energy value for each molecule node is used as weights and thecolors range from lower to middle to higher as from blue to yellow
to red.
Energy Inverted
The same weights are used but in this case the colors are inverted so
the lower values are more red and the highrte values are more blue.
This is for a more convenient identification of the molecules that areof interest.
Frequency
This mode draws the graph based on how often a molecule appears.
Betweenness Centrality
This mode is a measure of a node's importance. It is based on the ideathat a node is important if it lies on many shortest paths between othernodes in the network. The betweenness centrality of a node is definedas the number of shortest paths between all pairs of nodes in the
network that pass through that node.
Closeness Centrality
This mode is another measure of a node's importance. It is based on
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the idea that a node is important if it can reach other nodes in the
network quickly, either directly or indirectly.
Pagerank
This mode assigns a score to each node in the network based on the
structure of the network and the links between nodes. The basic idea isthat a node is more important if it is linked to by other important nodes
in the network.
Reaction Yield
This mode uses the yield values as weights for the network graph. Thismode also have some additional settings as explained below.

Figure 22: Using a different graph drawing mode, in this example the Betweenness
Centrality calculation.
How each mode is used, read and interpreted is very much up to the user/researcher studying the
network graph, and it is all up to them how they take what they see and find further.
The only mode that slightly differ from the other modes is the last 'Reaction Yield' mode, since it
contains a few more settings to play around with as explained below and can be seen in Figure 23.

Figure 23: The default Reaction Yield Network graph.
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The first setting (radio buttons) is based on the temperature applied to the reaction, either 200, 300 or
400 K (Kelvin) and draws the high yield nodes with a more warm and red color and the low or no yieldnodes with a cooler and blue color. Changing the temperature change the yield amount of the graphnodes, as can be seen and compared in Figure 24.

Figure 24: The yield values in a 400K reaction
The second setting (check box) allows the user to hide all low yield nodes and its edges for a lesscluttered view and better focus on nodes of importance. An example of this can be seen in Figure 25.

Figure 25: Only show high yield nodes and hide the rest.

Summary
We wish that this manual have told you anything and everything you need to know about SCAN Web
application and how to use it. Feel free to return here whenever your memory fails you on what to do
and when.
Congratulations on your newly gained status as a ‘SCAN-User’. Now it is time to do some serious
research. Enjoy!

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Index
AFIR..............................................................3, 4Atom......................................................9, 11, 25
Attributes.............2, 9, 11, 13, 14, 15, 16, 17, 25
Betweenness centrality....................................21
Chemical reaction..................................3, 4, 5, 6
Closeness Centrality........................................21
Contact Us.....................................................3, 7
Edge...........2, 3, 4, 5, 6, 9, 12, 15, 16, 17, 23, 25
Energy................9, 11, 13, 15, 16, 17, 20, 21, 25
Eq...........................1, 4, 5, 7, 8, 9, 11, 13, 15, 16Footer.......................................................2, 7, 25
Frequency........................................................21
Login...................................................2, 7, 8, 25
Logout...........................................................7, 8
Map search..........................................2, 7, 9, 25

Menu..............................................2, 7, 8, 17, 25
Mode......................................2, 9, 19, 20, 21, 22
Molecule 9, 11, 12, 13, 14, 15, 16, 17, 19, 21, 25
Networks...................................................1, 3, 4Node. .2, 6, 9, 11, 13, 14, 15, 17, 18, 19, 20, 21,
22, 23, 25
Pagerank..........................................................22
Reaction map...2, 4, 7, 9, 11, 12, 13, 15, 16, 17,
20, 25
Select...............................................2, 19, 20, 25
Sign Up........................................................8, 25
Temperature...............................................12, 23
Terms of Use.....................................................7
TS......................................................................9Yield....................................................15, 22, 23

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Figure Index
Figure 1: This is the first view that a SCAN visitor is met by.............................................................6
Figure 2: The Top Main Menu for the SCAN Web Application...........................................................7
Figure 3: The footer links are only available at the first front page.....................................................7
Figure 4: To the left is the Sign Up form, and for returning users the Login form to the right will be
used.......................................................................................................................................................8
Figure 5: If the user was previously and recently logged in, they will be automatically logged inagain.....................................................................................................................................................8
Figure 6: The Scan Map Search is the entry point for going further in to explore what SCAN has tooffer.......................................................................................................................................................9
Figure 7: The Search result showing the reaction maps that contains the chosen atom.....................10
Figure 8: The reaction map search result can be both sorted and ordered based attributes...............10
Figure 9: There are two types of views to use when looking at the 3D molecule..............................11
Figure 10: The full list of attributes that is contained within each reaction map...............................12
Figure 11: A list of all individual nodes in the reaction map..............................................................13
Figure 12: The nodes list sorted by energy values instead.................................................................13
Figure 13: The detailed view of a specifc molecule, reaction map node, with all its data attributes. 14
Figure 14: The list of edges this reaction map contains.....................................................................15
Figure 15: The detailed view of a specifc path, reaction map edge, with all its data attributes.........16
Figure 16: The Reaction map displayed as a node graph with each molecule node and it'sconnections edges...............................................................................................................................18
Figure 17: After the auto adjusting of nodes have stopped, each can be manually moved................18
Figure 18: When hover the mouse above a node it shows the molecule 3D view which the user caninteract with........................................................................................................................................19
Figure 19: A node and its neigbours selected.....................................................................................20
Figure 20: The shortest path between two nodes...............................................................................20
Figure 21: The different Graph drawing modes available..................................................................21
Figure 22: Using a different graph drawing mode, in this example the Betweenness Centrality
calculation...........................................................................................................................................22
Figure 23: The default Reaction Yield Network graph......................................................................22
Figure 24: The yield values in a 400K reaction..................................................................................23
Figure 25: Only show high yield nodes and hide the rest..................................................................23

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Thanks for your support