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OK - finally a bioinformatic coding problem that may not be so easy ...

former_member181923
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On this page here:

https://wiki.sdn.sap.com/wiki/display/EmTech/Bio-InformaticBasicsInRelationtoScriptingLanguages

I've defined Coding Problem 5 in Post 6 (6/27/2008.)

Very curious to see the answers/solutions that anyone provides for this problem - it's diferent than the problems previously defined.

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former_member181923
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Please note:

Readers of this thread should also take look at its continuation here:

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hi,

this doesn't work for several conceptual and technical reasons. Rasmol is much too inflexible. It is a pure desktop application and it cannot be operated via the commandline.

one would need a version which were an activeX control or java applet, which could be supplied with parameters from the embedding webpage or at least a version which were able to be initialized and operated fully over the commandline. latter wouldn't allow for a webapplication due to security restrictions but at least for a local scripted solution.

finally, embedding the whole thing into a webdynpro page would be another problem sincewebdynpro doesn't allow anything third party/customer specific to be sustainably embedded (by sustainably I mean more than a wholly isolated html frame or something).

finally, I ask myself, why on earth should someone want to use an SAP system for such an application? does it have anything to do with enterprise ressource planning? is netweaver suddenly known for its capabilities in scientific environments? is SAP software really open enough to support the many use cases in science where open source software is to be integrated sustainably?

wondering what this experiment is meant to illustrate...

anton

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Anton -

Thanks very much for your continued willingness to stay involved.

You raise a great set of questions and I will respond at length later today/tonight.

In the meantime - if you're interested - you might want to check out the wide range of "molecular viewers" available on the web. I think there's a list of them at the RCSB PDB site you're already familiar with. I am sure that more than one of them belong to the two categories you mention - embeddable control/applet.

Are you coming to LasVegas SDN Day? If not, do you have ShareView or a similar product?

It would be wonderful if you could some how be a part of any discussion that develops during my session on possible WDA bioinfomratic applications.

Best regards, and again, I'll respond to the main points of your post later today.

djh

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Anton -

Sorry I'm late in responding as I promised.

Will try to complete my response tonight and if so, will post back here letting you know that I've responded to your questions in the WIKI.

Best as always.

djh

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Also, please keep an eye out for a blog post on interaction of WDJ and/or WDA with three-dimensional visualization tools. ...

former_member181923
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AW -

I've responded here:

https://wiki.sdn.sap.com/wiki/pages/viewpage.action?pageId=27394166

This link contains a link to a recent blog post that I made regarding a certain kind of problem in maintenance logistics, and how this problem could easily be solved by better integration of SAP with 3-D visualization tools.

Best regards

djh

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Hi,

Read your blog about this issue and as a solution architect I find the topic of choosing front end technologies very interesting.

First some general thoughts on WDJ vs WDA.

The blog ["Everything you wanted to know about Web Dynpro but were afraid to ask, including..." |https://www.sdn.sap.com/irj/sdn/weblogs?blog=/pub/wlg/10206] [original link is broken] [original link is broken] [original link is broken]; takes up the question of which to choose, but basically answers that if your organisation and its competence is geared towards ABAP use WDA and if it more focused on Java use WDJ. I think this is a bit simplistic as there are some differences most which favor WDA; value help functionality built in, tighter coupling with backend, integration with SAP standard change and transport system (which is superior to NWDI). However, from a security point of view (external access) I like the WDJ approach better as you have a technology switch and less direct access to the core business system.

In your case I would see the WDA/WDJ application as the entry point for the end user. Here he/she is able to search for parts from the SAP Backend system. Standard properties such as weight, overall dimensions, vendor, etc. could be displayed here. The user could also trigger the 3d viewing of the part (along with other parts) in a separate section. The separate section could either be an iframe element within the WD (with reference to an non WD URL) or an iView in a portal which is called through for example client side eventing.

The 3d viewer is a black box with a single input, the 3d model of the structure, and a single purpose which is to display the part with possibility of rotating in 3d space. There is no output back to the calling application.

The above means that it is the WD applications responsibility to provide the input to the 3d viewer and the question is if WDA or WDJ is more suitable for this. I assume the 3d model is stored in SAP. IMHO they are both suitable for this. It might be that you need to convert the 3d model received from SAP to a format known to the 3d viewer. In this case there is a greater possibility that libraries to assist exist in Java and therefore WDJ might be preferred.

The 3d viewer itself does not belong as a part of a WD application. In order to provide sufficient functionality you need control over HTML code. If you the application is portal centric, I would recommend a simple portal component, if not a BSP would fulfill the requirements. It could also be hosted on any other web application platform such as Apache or IIS.

Regards

Dagfinn

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Hi Dagfinn -

I cannot thank you enough for your response ... apart from providing much important detail on app archictecture (e.g. iframes, portals, eventing), it legitimizes the question I was raising and the point I was making ... the idea that whatever SAP might do in ERP MM to provide "double 3D view" capability can be readily cloned for use in the bioinformatic context, even though we're dealing with "parts" in one case and "proteins" in the other case.

I've taken the liberty of pointing to your response here in my blog post also ... I hope you don't mind.

I also hope you don't mind if I start asking some detailed questions about the architectural elements you mention in your response.

Very best regards

djh

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No problem David, bring it on

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Dagfinn -

OK - you asked for it! (Just kidding.)

Seriously - to "concretize" discussion, I've posted an email (see below) to the PDB list server maintained by the RCSB/PDB consortium:

http://www.rcsb.org/pdb/home/home.do

I'm hoping I get at least one or two answers, and if I do, I can better specify the nature of the interface that has to pass parameters from the WDA/WDJ app to the molecular viewer.

Will post back if I get any answers.

Thanks very much again.

djh

************************************************

Email to PDB list-server:

************************************************

A small "skunk-works" group may be coalescing within the SAP community:

https://wiki.sdn.sap.com/wiki/display/EmTech/ScriptingLanguagesand+Bio-informa

tics

around the idea of an web application that can pop two mol viewer frames

simultaneously and let the user rotate the image in each to see "intuitively"

how they are similar/different. I need this app to streamline work for this

site:

http://strucclue.ornl.gov

and some at SAP already see the benefit of this type of application for the

purpose of comparing two components from the point of view of "substitutability"

or "interchangeability" (a big question in commerical and military logistics.)

My questions, therefore, are:

What mol viewer applet is best to call from another web applet when you want to

pass the viewer a PDB structure name, a chain ID, a "start" residue number, and

an "end" residue number? (The "start" and "end" residue numbers are for viewing of partial structures)

Will any current mol viewer applet take start/end residue numbers or would any

applet have to be passed a "tailored" PDB file with just the coordinate rows for

the residues in question?

Has anyone done anything like this already?

Thanks for whatever time anyone can afford to spend considering this matter and

for any information anyone can provide.

David Halitsky

StrucClues Site Team

615-613-2123

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Here is one answer to the question I posted at the RCSB PDB list-server (for the nature of this question, see my last post just above this one in this thread):

Hi,

SAP? For bioinformatics? That's amazing - I understood that SAP

started as an accounting package, and ballooned into

an "integrated solution" for, well, apparently anything.

Anyway, on to your actual question - there are many java applet

molecular viewers, but the one I would recommend is probably JMol:

http://jmol.sourceforge.net

because it has a very extensive feature set, is maintained, and is

quite well organized for use in the browser. To do the things you need

with JMol shouldn't be difficult as there is a scripting language for

JMol (that was inherited from RasMol) that can be used from

javascript.

Of course, there are other options, such as the excellent java mage:

http://kinemage.biochem.duke.edu/software/javamage.php

it depends on which features you need.

I will start a new thread in this forum regarding the best way to call javascript that calls an applet from WDA or WDJ.

djh