Design and Implementation of a Web Portal for a NeoCortical Simulator

1. 17th International Conference of Computers and Their Applications 2002 Authors • Kishor K. Waikul • Lianjun Jiang • E Courtenay Wilson • Frederick C. Harris, Jr • Philip H. Goodman University of Nevada, Reno Department of Computer Science Design and Implementation of A Web Portal for a NeoCortical Simulator http://brain.unr.edu

2. Introduction • Brain Computation Lab • URL: http://brain.unr.edu • This project is supported by the Office of Naval Research under grant 0000140010420 • What is the NeoCortical Simulator (NCS3) ? • Goal : Creating a novel classifier based a biologically realistic neocortical neural network. • Previous tools available : • NEURON • GENESIS • Features: • Object Oriented Design Enables to model the relationship among neurons • Parallel processing This is the key for approaching real time simulation • Clustering Algorithm Allows load balancing and data parallelism

3. Introduction • Hardware Overview • 30 Nodes with • 2 Pentium III processors • 4 GB RAM • 18 GB Hard disk drive • 2 Ethernet ports • All connected by Myrinet 2000 • High bandwidth for low latency network • 1.9 Gb/s network • NOTE: We just received announcement from the Office of Naval Research for additional funding that will allow to double the size of this machine.

4. Introduction Problems Advantages Of the web interface With text based interface • Access limited from the • local machine • Character based User • Interface • Manually writing the input • setting files, hence • complex • Prone to mistakes • Plotting results lengthy • and tedious process, • requires additional software • such as Matlab • Access from anywhere • Graphical User Interface • Complexities of creating object are hidden • Minimized chances of • mistakes as automated • Plotting results is as simple • as click and no additional • software required. • Need of the web interface for the simulator

5. Design: Web interface • Developed with PHP for front-end client, MySql as database • back-end on Redhat Linux operating system. • Sections: • User workspace • Administrative workspace • Requirements for user to get started: • User registration and authorization by administrator • A Java enabled browser

6. Design: Web interface • Steps to get started with the simulation • Sign in • Upload objects and setting files • or • Create objects • Create the input setting file from previously created objects • Configure and run the setup • Check status of running job • View results • Sign off

7. Design: Web interface : User Workspace Menu options • File : • file operations ,reports • and job status. • Objects : • construct hierarchical • objects • Runtime : • run job setup, check status of jobs. • Analysis : • plots of voltage and current , frequency transforms. • Help : • help on how to use the interface, samples

8. Design: Web interface : User Workspace Files options • New : • make new brain setting file. • Different File types • (based on data): • EPSC • IPSC • Spike setting • Brain setting • Open : • open existing files of any type. • Upload : • upload input setting files. • All the users can see each others files • View/Export : • check job status, download, plot data files. • Upload files to save configuration time • Own jobs can also be deleted. • Users can delete only own files • Delete : • delete unwanted files.

9. Design: Web interface : User Workspace dendrite dendrite dendrite Soma Synapse Axon Cell • Two categories of Objects: • Form based lowest level objects • Applet based hierarchical objects

10. Design: Web interface : User Workspace Reference object These are pre-created similar Objects, created by all the users including current user. Using reference objects can really accelerate the process of creating new objects. Element based help • Lowest level objects : • ( Anatomic and Physiological elements) • Do not contain any other objects • Form based input • Input may contain more than a single parameter separated by spaces • Online help for each input element of the object

11. Design: Web interface : User Workspace hierarchy Reference objects • Higher level objects (Constructs) : • Contain low level objects • Hierarchical construction with applet • One input element may require several dependent parameters

12. Design: Web interface : User Workspace Control Panel Common operations • Control Panel • Easy access to common operations such as save, edit and delete. • Objects by default are • temporary, unless saved • Edit and delete allowed • only on own objects • Refresh to update values

13. Design: Web interface : User Workspace • Status Message Panel : • Used to show messages critical to the last done operation Status Message Panel - message box • Error messages • Alerts • Suggestions for the input • such as correct format

14. Design: Web interface : User Workspace These options require administrative password as critical to performance of server. • Runtime settings : • Run setup : • Start new job • Check status of running jobs • Advanced settings • Email notification on completion • Choose Server to run job • Network to run : Ethernet / Myrinet

15. Design: Web interface : User Workspace List of files that were added but now be removed List of files that can be added • Runtime settings : • Edit brain settings : • Change default command line arguments • Change brain input setting file • Specify setting files directly • Add/remove files

16. Design: Web interface : User Workspace • Results Analysis : • Current and Voltage Displays : • Plotting data from simulations • PHP generated PNG image sent to the • browser • Better than Java applet approach • Plotting program keeps a cache for recent • plotted data

17. Design: Web interface : User Workspace • Help : • Java applet based hierarchical help menu • Comprehensive help on each menu and how to • use the interface • Description of the current composition of • objects • Complete examples of the setting files • Definitions of the terms

18. Design: Web interface : Administrative Workspace Options • Administrative controls : • Edit format of the objects • Maintenance of the tables by description • MySql Database administration • Job monitoring • Add/Remove users

19. Design: Web interface : Administrative Workspace • Object Format : • Change number of parameters • Data type, number of values and boundary • values used for JavaScript validations • Description appears at the popup help as well • as applet based comprehensive help First select object from list Select attribute of object

20. Design: Web interface : Administrative Workspace • Table descriptions : • A table of description of tables • Maintains special notes on tables about • structure • Great help for programmers

21. Design: Web interface : Administrative Workspace • MySql Database Administration : • A web based client (third party application) • Access to the database from anywhere • Platform independent interface • Query-less table manipulation • Allows to run queries List of tables List of tables

22. Design: Web interface : Administrative Workspace • Job monitoring : • Check status of jobs • Filter jobs by user name, server name or brain name • Delete jobs from waiting queue • Change priority of the jobs in the waiting queue Job Filter

23. Implementation Issues: • Database Design : • Standard for naming tables as applet based interface involves lot of parsing • e.g. “brains_table” means table for brains objects, similarly all hierarchical objects will have • name in the format <object_name>s_table • Standard for naming columns of the table to simplify data retrieval • e.g. “type_0” means attribute name is type and input for this attribute is simple form • “connect_1” means attribute name is connect and it’s a hierarchical input. • standardizing these names helps a great deal while writing generic • code for all objects • Data stored in compressed form and decompressed on the fly while retrieval

24. Implementation Issues: • Communication issues: • Remote control and monitoring of the simulator • Dynamically generated scripts on the head node • Parameters and input files retrieved from database Job submitted to the daemon with all parameters and data Database Waiting queue User TCP socket Daemon Input files, parameters Query waiting queue Connect message Object Data tables Run Job Upload log, results User: Web browser Querying results

25. Implementation Issues: • Security issues: • Application Level Security • All transactions encrypted with SSL, tested with OpenSSL • Web server separated from simulator ( fire-fence) • User level Security • Trusted environment • Users can edit/delete only own files • Encrypted user passwords stored in database • System level security • Removal of unused extensions and programs • Security patches to the web server, operating system.

26. Future work: • Enhanced security with SSL • Java applet based help • Auto-wakeup daemon to linearize currently triangular • relationship.

27. Thank You

28. Questions ???