Release 2.9.0
The primary goal of this release was to add an interactive, visual representation of the reaction modeling used by the search engine to the interface. This goal was accomplished by adding two new sections: 1) a search page where the user can provide parameters and keywords to search both name defined reactions and rule defined reactions (see below) 2) a page where the user can then view the details about one specific reaction.
A clarification of the difference between the two types of reactions that are used by the search engine follows. The first type of reaction, the name defined reaction, is modeled by using the IUPAC names of both the start and end molecules, along with the name of a reagant or catalyst used for the reaction, and any additional reactant or product molecules. It is meant to apply SPECIFICALLY to the one molecule named as the starting molecule. An example of a reaction modeled this way is the first reaction of the Calvin cycle. This particular reaction can only be applied to Ribulose 5-phosphate. In general the pattern of this reaction type is used for specific biochemical life reactions. It is also a MUCH simpler type of reaction to model because the search engine will only need to look for reactions with a matching start molecule name.
The second type of reaction, the rule defined reaction, is modeled as two sets of two types of rules and is more complex. The first type of rule, the location rule, determines whether or not the particular reaction can be applied to a particular molecule. The criteria used to make this conclusion are that the particular molecule contains all of the special conditions listed in the location rule (such as that the molecule is aromatic) and that the molecule contains one or more of the functional groups listed in the rule. The location rule allows the reaction type to apply to a BROAD class of molecules as opposed to just one molecule like the first type of reaction.
The second type of rule for the rule based type of reaction, the reaction rule, defines what applying the reaction to a particular molecule actually does (as opposed to simply listing the name of the product molecule). It consists of four parts: 1) an action verb, such as "add", "replace", or "remove" describing the overall action of the rule, 2) the first functional group involved in the reaction including the type of Carbon that functional group is found on, 3) any specific location instructions for the action, and an optional 4) second functional group involved in the reaction (for the "replace" action this is the functional group that will replace the functional group from the second part).
This second type of reaction, based on the two previously explained rules, can contain one or more instances of both types of rules. An example of a reaction modeled using the second type is the oxidation reaction involving Potassium Permanganate. The location rule for the oxidation reaction in this case is to find any molecule containing a primary alcohol. The reaction rule for the reaction is to replace any primary alcohol with a carboxylic acid functional group. As this type of reaction requires the search engine to match a molecule by rules (in this case a molecule containing a primary alcohol) rather than by name, this process is more complex. This second type of reaction ALSO is modeled additionally by keeping track of any reagants/catalysts used.
The page to view the details of the first type of reaction, one example being the first reaction of the Calvin cycle, is pretty self explanatory. It contains all information involved in the reaction including the IUPAC names of the start and end molecules. It is also possible to view the molecules involved in the reaction by clicking the "View Reaction" button at the bottom of the screen.
The page to view the second type of reaction, one example again being the oxidation reaction involving Potassium Permanganate, is slightly more involved. In addition to being able to view the details, you are able to view further details about each rule involved by clicking on the particular rule. This further granularity was added to the interface anticipating support for a user to edit and add rules of both the location and reaction types in the future. Also, the page supports a functionality to test the reaction. By clicking on the "Test Reaction" button the user is able to enter a molecule name, click the search icon to view it, and then click the reaction icon (beaker) to view the molecule resulting from applying the reaction.
Standards - IUPAC naming standards again were followed. No further new standards have been applied for this update.
Controls - Use of the search page is generally self-explanatory. It was designed to use functionality similar to search bars found in other modern web sites. The user is also able to refine a search by the type of category of the reaction and the reagant used in the reaction. Clicking on the pencil/edit icon allows the user to view the more detailed view page of each rule. Use of the view page is also pretty straightforward. For the type of rule based on the start and end IUPAC names of molecules, the user can click on the "View Reaction" to see a visualization of the molecules involved. For the type of rule based on the location and reaction rules, the user can click on each location and reaction rule for further detail. The user can also click on "Test Reaction" to view the result of applying the particular reaction to a molecule.
Future Considerations - An obvious future plan is to allow the user not only to view reactions of both types, but also edit them and create NEW reactions. The "Test Reaction" functionality in this case will provide useful for exploring how a new rule will apply to a particular molecule. Finally, I anticipate refining the search page a bit more.
The primary goal of this release was to add an interactive, visual representation of the reaction modeling used by the search engine to the interface. This goal was accomplished by adding two new sections: 1) a search page where the user can provide parameters and keywords to search both name defined reactions and rule defined reactions (see below) 2) a page where the user can then view the details about one specific reaction.
A clarification of the difference between the two types of reactions that are used by the search engine follows. The first type of reaction, the name defined reaction, is modeled by using the IUPAC names of both the start and end molecules, along with the name of a reagant or catalyst used for the reaction, and any additional reactant or product molecules. It is meant to apply SPECIFICALLY to the one molecule named as the starting molecule. An example of a reaction modeled this way is the first reaction of the Calvin cycle. This particular reaction can only be applied to Ribulose 5-phosphate. In general the pattern of this reaction type is used for specific biochemical life reactions. It is also a MUCH simpler type of reaction to model because the search engine will only need to look for reactions with a matching start molecule name.
The second type of reaction, the rule defined reaction, is modeled as two sets of two types of rules and is more complex. The first type of rule, the location rule, determines whether or not the particular reaction can be applied to a particular molecule. The criteria used to make this conclusion are that the particular molecule contains all of the special conditions listed in the location rule (such as that the molecule is aromatic) and that the molecule contains one or more of the functional groups listed in the rule. The location rule allows the reaction type to apply to a BROAD class of molecules as opposed to just one molecule like the first type of reaction.
The second type of rule for the rule based type of reaction, the reaction rule, defines what applying the reaction to a particular molecule actually does (as opposed to simply listing the name of the product molecule). It consists of four parts: 1) an action verb, such as "add", "replace", or "remove" describing the overall action of the rule, 2) the first functional group involved in the reaction including the type of Carbon that functional group is found on, 3) any specific location instructions for the action, and an optional 4) second functional group involved in the reaction (for the "replace" action this is the functional group that will replace the functional group from the second part).
This second type of reaction, based on the two previously explained rules, can contain one or more instances of both types of rules. An example of a reaction modeled using the second type is the oxidation reaction involving Potassium Permanganate. The location rule for the oxidation reaction in this case is to find any molecule containing a primary alcohol. The reaction rule for the reaction is to replace any primary alcohol with a carboxylic acid functional group. As this type of reaction requires the search engine to match a molecule by rules (in this case a molecule containing a primary alcohol) rather than by name, this process is more complex. This second type of reaction ALSO is modeled additionally by keeping track of any reagants/catalysts used.
The page to view the details of the first type of reaction, one example being the first reaction of the Calvin cycle, is pretty self explanatory. It contains all information involved in the reaction including the IUPAC names of the start and end molecules. It is also possible to view the molecules involved in the reaction by clicking the "View Reaction" button at the bottom of the screen.
The page to view the second type of reaction, one example again being the oxidation reaction involving Potassium Permanganate, is slightly more involved. In addition to being able to view the details, you are able to view further details about each rule involved by clicking on the particular rule. This further granularity was added to the interface anticipating support for a user to edit and add rules of both the location and reaction types in the future. Also, the page supports a functionality to test the reaction. By clicking on the "Test Reaction" button the user is able to enter a molecule name, click the search icon to view it, and then click the reaction icon (beaker) to view the molecule resulting from applying the reaction.
Standards - IUPAC naming standards again were followed. No further new standards have been applied for this update.
Controls - Use of the search page is generally self-explanatory. It was designed to use functionality similar to search bars found in other modern web sites. The user is also able to refine a search by the type of category of the reaction and the reagant used in the reaction. Clicking on the pencil/edit icon allows the user to view the more detailed view page of each rule. Use of the view page is also pretty straightforward. For the type of rule based on the start and end IUPAC names of molecules, the user can click on the "View Reaction" to see a visualization of the molecules involved. For the type of rule based on the location and reaction rules, the user can click on each location and reaction rule for further detail. The user can also click on "Test Reaction" to view the result of applying the particular reaction to a molecule.
Future Considerations - An obvious future plan is to allow the user not only to view reactions of both types, but also edit them and create NEW reactions. The "Test Reaction" functionality in this case will provide useful for exploring how a new rule will apply to a particular molecule. Finally, I anticipate refining the search page a bit more.
