Dr. Dieter W. Lorenz

Dipl.–Inform. Alexander Rüegg

Bielefeld University

Department of Bioinformatics

EDMEDIA, Honolulu © 2003

Generic Biological Learning Laboratories

GenBiLL

Outline

GenBiLL: Generic Biochemical Learning Laboratories

1. Motivation

2. ViSeL: Virtual DNA Sequencing Laboratory E-Learning Concept Teachware Modules Field Test: Evaluation Results

3. Generic Approach: Laborator – The Laboratory Generator Aims Realization

4. Conclusion

5. Acknowledgement

Aim of GenBiLLGeneric Biological Learning Laboratories

ViSeLVirtual Sequencing Lab

Production & Evaluation

LaboratorLaboratory Generator

WebXamTest Series Generator

UniMuGUniversal Multimedia Glossary

ViSeL • OverviewThe Virtual DNA Sequencing Laboratory

ViSeL • Tutorial

ViSeL • Glossary

ViSeL • Web Component

ViSeL • Simulation Environment

ViSeL • In Educational UseStudents, Wegberg, Germany

ViSeL • Overall Results Good Structure, arrangement and orientation within the whole learning environment (Ø2,2)

Realistic and successful construction of the virtual lab

Intuitive handling and easy drag & drop interaction within the lab simulation part

Need for more visual feedback in the lab

Desire for step by step explanation for each work step in the lab

Obviously high motivating impact

Fun factor was rated higher (Ø1,3) then potential use (Ø2,6)

Large compensation of missing technical infrastructure

Useful completion to theoretical and practical teaching (100%)

Every person recommended the programme

GenBiLL • Generic Developments

Second Aim: Reduce enormous expenditure to create biochemical laboratory

learning environments with generic methods.

UniMuG

Tool to create multimedia glossaries

WebXam

Tool to create learning target evaluations for the WWW

Laborator

Tool to create laboratory simulation environments

Laborator • Lab Generator

Aims:

Based on the experiences collected during the production process of the ViSeL interactive laboratory module:

Offer an object oriented framework (IDE) to design individual biochemical screen experiments on the fly. No programming skills necessary!

Simulate quantities of thermodynamic parameters – T, p, [Ai], t,….

Provide the basic learning units and a large supply of laboratory objects and devices.

Laborator • Realization

Laboratory-Allocation-Frame

L = ( T, O, U, R, I )

T = Theme

O = Set of laboratory objects

U = User Interaction

R = Rules for the behaviour of objects and chemicals

I = Optional rules for user interaction limitation (guided tour)

Laborator • RealizationTheme T

Which working place? – Which Security Level?

Laborator • Realization

Abdampfschale Abfalleimer Abtropfgestell Ampulle AnalyseStoffMelder Becher Becherglas Brutschrank Bunsenbrenner Chemikalienloeffel Destillationsgeraet Dispergiergeraet Dose Entsorgungskanne Eppendorfgefäss Erlenmeyerkolben Exsikkator Fass Flasche Gaswaschflasche Gefriertrockner Gluehschaelchen GluehschiffchenHeizbad Heizhaube Heizofen Heizplatte Homogenisator Inkubationsschuettler Isolierkanne

Kanister Kasserolle Kolbenprober Kuehltruhe Kuevette Kulturglas Laborloeffel Labormixer Loeffel Loeffelspatel Magnetrührer Mastercycler Messbecher Messkolben Messpipette Messzylinder Moerser MultiLineInfo Petrischale Petrischalendrehtisch Pipette Pipettenflasche Praeparateglas Reagenzglas Reaktionsgefaess Reinigungsautomat Rotationsverdampfer Rundkolben Saugflasche Saugrohr

Schüttelgeraet Sicherheitsbehaelter Sicherheitsgefäss Spritze Spritzflasche Stahlschale Sterilisator Stutzenflasche Teclubrenner Teller Thermostat Tiegel Trennkammer Trockenschrank Tropfflasche UV_Lampe Uhrglasschale Vierkantbehaelter Vierkantflasche Vollpipette Wasserbad Weithalsbehälter Weithalsflasche Weithalsglas Zentrifuge Zentrifugenglas Zylinder

~ 90 predefined Objects (In German):Laboratory Objects O

Dra gO b je c t

O b je c t

Eva p o ra ting d ish Bunse nb urne r

Sub sta nc e Pa ra m e te r

In te ra c tio n

Rule

C e llsInEp p iRule

Dra g Ap p le t Dra g Fram e

DNA-Iso la tio n La b

<<uses>>

<<

instantiate

s>>

Application type

1..*

0 ..*

2 0..*

1..*0..*

La b o ra to ry

+action(obj1: D ragObject, ob j2: DragObject): void

Rule In te rp re te r

+Infere( ob j1: ob ject): vo id <<executes>>

Ve sse l

+decantTo( ob j1: ob ject): vo id

De vic e

+applyTo( ob j1: ob ject): vo id

C la ss-Fram ewo rk

<<uses>>

....

.... .... ....

Laborator • Realization

Gray-colored region:Core elements of the generic laboratory model,containing all essential rules for interpretation of user interactions.

User Interaction Interpreter U

Laborator • RealizationRule Interpreter for R , I

Combining Operator:

(N)AND/(N)OR

Combining Operator:

AND

Actions

Actions AND Conditions

Conditions

Laborator • RealizationInterface for R , I

Laborator • Bringing it all together

VLML – Virtual Laboratory Markup Language

1 <model name="isolation-laboratory">2 <listOfCompartments>3 <compartment type="vessel">4 <name>eppendorf-tube</name>5 ...6 <listOfSubstances>7 <substance name="E1" pH-value="4.5">8 <stateOfAggregation>liquid</stateOfAggregation>9 <quantity unit=”mol”>0.1</quantity>10 ...11 </substance>12 ...13 </listOfSubstances>14 </compartment>15 ...16 </listOfCompartments>17 <listOfRules>18 <rule type="interaction">19 <name> Fill-E1-in-Eppendorf</name>20 ...21 </rule>22 ...23 <rule type="reaction">24 <name>E1+E2->P1</name>25 ...26 </rule>27 ...28 </listOfRules>29 </model>

Laborator • Creating New Labs

1. Define the set of devices and instruments participating the work process

2. Define the set of receptacles and containers participating the work process

3. Define initial parameters for devices and receptacles

4. Define the set of chemical substances in certain receptacles

5. Define reaction rules depending on chemical substances and thermodynamic parameters

6. Define rules for guided tour (Optional)

7. Use Laborator-IDE

Carry out the following steps:

Laborator • IDE

Laborator • Example

Isolation Lab – WWW-Version 1.0

GenBiLL • Conclusions

1. Virtual learning laboratory environments can help to improve the quality of education: personalized training, time independence, higher motivation and resource saving.

2. To what extend methodical competence is encouraged still has to be verified in comparative evaluations.

3. In any case: Students learning success depends on embedding this kind of media into a wise curriculum.

4. To reduce the high amount of human and financial endeavour flowing in the development of such learning environments suitable generic tools have been successfully invented.

5. With Laborator it is possible to build up platform independent, highly interactive biochemical laboratory experiments in accurate time without any programming skills.

6. We consider GenBiLL as a major step into systematic generic construction of virtual laboratories for different scientific fields.

Acknowledgement

Prof. Dr. R. Giegerich

Prof. Dr. Alf Pühler

Prof. Dr. W. Pipersberg

Prof . Dr. U. B. Priefer

Prof. Dr. A. Steinbüchel

Dr. C. Schleiermacher

Dr. W. Arnold

Dipl. Inform. A. Reckmeyer

Dipl. Inform C. Rezazadeh (FH)

Prof. Dr. R. Hofestädt

Dipl.- Inform. A. Dieckmann

M. Egerding and his Students

T. Schmidt

Dipl. Inform M. Niemann

Dr. T. Nattkemper

Dipl. Inform. S. Lorenz

T. Kugel

And all the others...

Any Questions?

www.vlab.de

Thank You!

Dr. Dieter W. Lorenz

Dipl.–Inform. Alexander Rüegg

Bielefeld University

Department of Bioinformatics

EDMEDIA, Honolulu © 2003