A Research Management Tool for BID

A Research Management Tool for BIDDeveloped at:

College of ComputingGeorgia Tech

1Finding and understanding relevant biology articles

Sharing articles with team members

Sharing my understanding of articles with team members2Bio-inspired sea water desalination technology

Jeeves

Wooster

GussieConsider the following scenario. Jeeves, Wooster and Gussie are part of a design team and their design problem is to conceptualize a novel bio-inspired sea water desalination technology.3

Jeeves

Jeeves comes across this article which he thinks is valuable to his design4

Jeeves

Log inJeeves logs into Biologue5

Jeeves

Jeeves CollectionJeeves sees his workspace with previously entered articles6

Jeeves

Add new entry1He clicks on Add new entry button7

JeevesAdd new entry

Enter basic info12

He enters some basic information about the article like author, title, publication information etc.8

JeevesAdd new entry

Enter basic info12

Upload the file3Save4He uploads the PDF file by attaching it to this entry. He saves this information.9

In Biologue, you can also tag the article with SBF information, which you will see next.10

JeevesFunc.A. Ileum transports Na and Cl ionsFunc.B. Ileum transports waterComing back to Jeeves, lets assume that Jeeves has read the article. Jeeves identifies the two main functions of rats Ileum in this article.11

Jeeves

ClicksHe clicks on the SBF info. tab at top here. He sees three buttons at the top (1) Add top-level function, (2) Add sub-function, and (3) Remove function12

Jeeves

Clicks Add top-level FunctionHe clicks on Add top-level function button and a textbox appears. He types his function name. Note that this has autosuggest feature, which means that as you start typing the name, if a similar function has been created by you or someone else in the past, you can reuse it. Reusing things is highly encouraged.13

Jeeves

Clicks Add top-level Function

Now Jeeves has created his first top-level function14

Jeeves

Now Jeeves sees these three things at the bottom. Fn stands for information related to function, Bh for information related to behavior and St for structure.15

Jeeves

Jeeves first enters Function related information here, which is captured as an Subject Verb Object expression. The subject of the function, or the thing doing the function here is Ileum. The verb or the action associated with this function is Transport, and the objects on which the Subject acts are sodium ions and chloride ions. Makes sense?16

Jeeves

Jeeves then enters Behavior related information. This is basically a short textual description of the mechanism by which the function is identified. The mechanism in this case is Active transport, and he gives a short description of how active transport occurs in this context.17

Jeeves

Similarly, Jeeves then enters Structure related information, which is a short description of the various parts the comprise the active transport system in this case.18

JeevesNow Jeeves creates another top level function for Ileum transports Water19Func.A. Ileum absorbs Na and Cl ionsFunc.Ai. Ion attaches to pumpFunc.Aii. Pump changes orientationFunc.Aiii. Ion detaches from pump (release)Func.B. Ileum absorbs waterFunc.Bi. Move water along concentration gradientFunc.Bii. Create hydrostatic pressureFunc.Biii. Move water across concentration gradient

JeevesJeeves likes this SBF stuff. Now he identifies these many subfunctions associated with each top-level function he created.20

JeevesNow Jeeves add those sub functions to create this hierarchical SBF structure, with each level having its own Function, Behavior and Structure information.21

Log in

WoosterwoosterNow, lets assume that Wooster logs in.22

WoosterJeeves CollectionWoosters CollectionNow, in addition to seeing his own collection, he also sees Jeeves collection. Not only that, he also sees Gussies collection because he is also part of the team and also the entire class collection.23

WoosterWooster clicks on the latest paper that Jeeves has added. In addition to seeing its basic info (not shown here), he also sees the SBF information associated with that article as shown on the right. Just by glancing this SBF view, he builds a quick mental model of not only what system this paper is talking about (the Ileum), but also how it works. Now he does not need to painstakingly read the entire paper to understand how this system works and make a decision about whether the paper is useful to him or not.24

WoosterNow Wooster is curious about one particular function, that is how the Ileum transports the ions, which is highlighted here. He wants to how exactly this function is achieved.25

Wooster

ClickHe clicks on the small bh button in the function box, which opens up a dialog that shows the mechanism used by the Ileum to achieve that particular function.26

Jeeves

WoosterShared the articleShared their understanding of the articleWooster need not read a 40 page journal articleJeeves and Wooster not only shared an article of interest, but also shared their understanding of the article in some common vocabulary. The key is this common vocabulary, which helps Wooster quickly grasp the information content of the article.27Search featureStandard bibliographic queriesQueries related to the SBF stuff: query onFunctionsSubjects and objectsVerbs or actions

There is a simple search feature included in Biologue as shown here. In addition to querying on standard bibliographic information like author or title, you can also query on SBF related stuff. You can query on functions - e.g., find all the articles related to transporting water. You can query on Subjects and Objects - e.g., find all articles related to Basilisk lizard, Ileum, etc. You can also query on Verbs or actions - e.g., find all articles related to propel, adhere, filter, etc.

Every search result not only returns the article, but also the SBF view of that article. Imagine searching Google Scholar and getting SBF diagram as part of the result set. That is what we are trying to achieve here.28Search featureSmall seed library177 articles from BID class of 2008Not all of them annotated with SBF stuffSearch feature may not be very useful right now but becomes useful over time

29Closing thoughtsSimple little appBeta release in two weeksUse it and give us feedbackDownload and usage information will be provided in the class in coming weeks

30