Interfacing the JChem Suite outside of Java (Web Services, .NET, SQL, Workflow platforms)Presentation

September 2010 Author: Jonathan Lee (ChemAxon)

Product JChem Web Services Product group IT platform toolkit

Understand and decide your best interface from the many non-Java programming interfaces to the JChem Suite of tools. Many interfaces will be discussed, such as the pure .Net interface, Oracle Cartridge, Web Services, and workflow platform integrations.

Subtitle for hearing impaired (hide)

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Good morning

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am a little stuck in

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Budapest but actually it’s not stuck I actually like it

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so again I know it’s early

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but I want to say good morning, good morning Ivan

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good morning Pat

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good morning to Dan

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morning Brett

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what I want to say is

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we at ChemAxon like to

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think that we can provide

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for

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each individual

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situation, each individual

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platform

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or technical decision

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and

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with JChem

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we’ve provided a whole number of interfaces to be able

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to allow you guys to do that

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again my name is Jonathan lee

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I’m the project manager of JChem Base our database product and

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Web Services product

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so I’ll talk a little bit about the interfaces

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maybe what’s most important to you guys is the situational factors

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what it is

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what kind of questions that you have

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what kind of doubt that you have

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in your mind when you’re deciding on

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how can I use JChem

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the SQL interface the .NET interface

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Web Services interface

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work flow, pipe-lining tools

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will go over that

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in small details here

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so… on this side

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is all the

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suits of tools that ChemAxon

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provides

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in JChem

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you will hear

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about Marvin today

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you’ve seen

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in

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various talks

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starting off

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yesterday about all the different

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little pieces and tools

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all this little great icons that we’ve got

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put into

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the applications

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that he’s made

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and I’d like to make sure that you know that hey

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you can get your application

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to hooking with all the things that we’ve made

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and that you’ve heard about

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today and yesterday

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so of course

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Dan Durkin said yesterday that how he loves

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ChemAxon because it’s got Java interfaces and it just works works well

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so yes of course

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we work well with playing with Java objects

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we work well with

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service like JSP

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and what I’d like to remind you is that

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yes you can do that but you can also do all these other things

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use SQL

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with our Cartridge product

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work with the .NET framework

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all of the things

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that you can do in Java

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just about everything you can do in the .NET world

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and that’s what really makes you leverage of the

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or use as leverage

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of your platforms that you have

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at your own businesses

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of course Web Services is something near and dear to my heart

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but

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that allows us to say hey you can use JChem but be independent of your platform

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be independent of your

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programming language

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and work with a lot of the

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infrastructure that you’ve built in

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in your own companies

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so what are some of the situational factors that you’ve got

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in fact actually the slide really talks about well… maybe

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all of you here

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you’ve heard about a lot of things that you want to try out you’ve heard about things

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that

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you think that’s actually going to have a good fit

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but maybe you’ve got other folks at your work place that you have to convince

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or you have to

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quarrel the doubts that they have

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and we’re going to say well they have a lot of questions and you’re gonna have answers

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for them as well

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what if we don’t use Java well

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you ask for what actual

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language do you prefer

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you’ve got the .NET

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other web languages that are just

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a forefront for web2.O stuff

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Web2.O stuff

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if it’s going to use

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SOAP or if it’s going to use

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any kind of well

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or it’s going to have any kind of web

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friendly

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libraries then yes of course you’re going to be able to use JChem

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does your environment have just Oracle

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we handle it

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Cartridge

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if it does it that’s fine too

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we’ve got all sorts of connections

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with the JChem suite of tools

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so that shouldn’t be a question about we don’t have

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Oracle so we can’t use this or that

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all the stuff that’s provided

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in the Cartridge

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for example you can also do inside of JChem

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the end user environment

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all we need a desktop application we have products that do that, InstantJChem

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if you want the Web Client, we also have products that do that

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we’ll talk about the other similar things in the future

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about how you can do that the best of

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your situation

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and of course some of our folks out there

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have a service-oriented architecture well that’s that’s actually perfect for

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the Web Services

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that’s perfect for

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building up in re-using all those components and Web Services

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so JChem Cartridge

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that’s a product that

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is entirely tied with the Oracle database of course that’s one of the

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most used

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databases

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of our customers

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but we’ve leverage that system

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being able to use the security and the

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reliability, scalability

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of Oracle

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we also provide

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store procedures

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to handle the database work

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and JChem server to handle things that are outside of that route so maybe it’s

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done better outside of

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the Oracle database

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so we separate the

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work

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to the

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best

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machines

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so

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we’re supporting SQL in that sense

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as as a programming language out so that again we’re talking about data bases outside of Java

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but if you prefer to use the SQL language

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this is something you can use

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and we also support mostly JChem modules in this JChem Cartridge product

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in .NET we’ve made great leaps and bounds

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over the past year too

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to support the .NET framework

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we’re using the

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IKVM

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technology but

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basically we’re transforming

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directly from the Java into the .NET format

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so it’s a lot faster

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and

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and much more compatible

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Marvin applications are in there,

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Marvin View Marvin Sketch

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and as you can see in the

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graphic there

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we’re using that code

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to develope for

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JChem for Excel

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JChem for SharePoint

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and so

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we know it works and you guys can use it as well

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here the .NET stuff of course supports .NET languages

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and all the JChem suit except for

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Cartridge

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which we’ve talked about earlier and Marvin Beans

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Jchem Web Services

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is

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what I would like to think

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that has interoperability as its

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main

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point

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we want to make sure that we use all the standards

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in the industry

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like WSI, SOAP and WSDL

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and allow

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everybody to use

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this outside of Java world

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but inside of the web world

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anybody that is using web clients and wants to use

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friendly

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languages can do that

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AJAX, JavaScript

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Perl, Python, Scripting Languages

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Ruby, PHP

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we have Adobe Flex folks

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a lot of choices here

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and you just want to

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utilize what your company

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has strengthened

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of course you can still use them languages with Web Services like a

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Java

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we have a growing list of models every time we’re making a new model

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we’re going to try and put that into Web Services

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great thing about Web Services that it’s automated client generation so you’re

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doing

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the heavy lifting you’re not doing it we’re doing it

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or the SOAP

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languages or library they come with

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all these languages

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you can use that

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and you wouldn’t have to worry about any of the

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interoperability issues

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I talked a bit about SOAP

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and that’s what’s unlocking

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all of this

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all these interoperability

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blocks of problems

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here you can see

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with this amount code

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and Python with this amount of code JavaScript

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gets translated into something

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like this it’s called SOAP this is the lingua franca of Web Services

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and when you get to use JChem Web Services and of course

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although the rich

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chemical intelligence inside of the JChem suit

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so this is really unlocking it

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unlocking all that intelligence for you

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just a quick

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mention about the architecture

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because i want to make sure that

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it’s it’s clear that you can use

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Web Services on any platform

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with any language we’re using open source components a cynical access to and Tomcat

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you may have heard that in the tech circles

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and here in this red

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what that allows you to do is that hey we can use it on any

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OS, any platform anything that runs Java

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and it’s open source so you get that support of that community

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and the price tag

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a list of all the features here

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we talked about features

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in Cartridge in the .NET

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but here again we have a growing list of these services

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since I’ve been doing this

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a little while

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this list is actually too long for my slide here

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and these future services are coming

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there very soon in 5.4

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the ones that we’ve always

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database related services JChem searching

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data manipulation, all these

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DML, DDL type of functionality

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loading and unloading tables, importing & exporting that sort of things

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Molecular Conversion Services

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Standardization

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these are is a great for registration

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services

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or applications Chemical Terms something that is great for virtual screening

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and Reactor services creating things that are

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chemically visible

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a whole bunch of things that I’m excited about

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that is

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coming in a month or two

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molecular search Markush is something that we’ve got coming up

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in 5.4

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JChem table management

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couple of things you can see up there

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and those are coming a little bit later

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I’ll show you a quick demo

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and the point of the demo is just

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well for me is to show a little of what we’ve done but

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to show you yes

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this is all made in

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in a non Java environment

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it uses the Web Services

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it’s got a whole number

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might have to go and click on the

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user

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the point of the demo’s is to show that hey we can

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create full future applications

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and still get all the features that JChem provides

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but we do it outside the Java

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so my point is that you’ve got a lot of options

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and you’ve got a lot of chemical intelligence that you get ripped out of JChem and put it

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anywhere you want

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use that Marvin

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use the

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Markush stuff

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that you’ve heard about

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well the other things that I want to show you was yes it was that easy

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I guess I downloaded

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the 5.3.8 the latest release

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on one configuration page I just changed right pointed to the

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database

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that I wanted to point to and I just double click on start up top at so

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very easy this is an application a demo

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and actually pretty full-featured application that comes through

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with Web Services server

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and you can go and use it

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OK, there is a quarter of a million structures

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in this large data base

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and if you can see

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when we flip down

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browsing is very very fast

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the great thing about

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the great thing about this application here is that we’re using AJAX and where using any of the libraries

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that

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AJAX well all of that

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community

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provides you when we’re using jQUERY

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Windowing system so

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you get to use whatever your developers like to use

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OK I wont treat you much on this now

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I think the point is made last thing I want to say is is work flow integrations

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for the computational chemist for the folks that like the work flow

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work flow tools to build your own workflows and send it off to your own colleagues

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we support all these major work for integration tools pipeline pilot

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we provide those directly

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we dump the modules

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the modules here

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actually this one!

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and KNIME

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provided by Infocom

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and Inforsense which is done by IDBS

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lot of information on the web sites

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that’s actually a great

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source of

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of information

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we have stuff about Cartridge we have stuff about .NET

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and we have stuff about Web Services

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and these forms a really important for the developers

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so that they have instant

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communication with us

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okay well thank you very much that was my talk hopefully you’ve seen that yes

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you can make these things out of Java we’re not just a Java shop

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and that we can get

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your applications to use ours

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Great, thank you

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We have time for one or two questions if anybody has some few questions for Jonathan

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(Questions from the spectators)

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I’m very curious about the Web Services as well as the nodes and components for

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the work flow tools

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going forward as you release new

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either you know pieces of your infrastructure as Web Services do you intend to deploy a parallel

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nodes to Pipeline Pilot and KNIME or do you recommend that going forward you know we just

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use the native capabilities of those tools and connect to the Web Services directly

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I see, trying to connect to the Web Services through

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like Pipeline Pilot node or through KIME nodes that’s corrected if you deliver a nodes

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you put sort of your framework around it what we intend to use and what may be black box

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whereas if we go to the web service we have more control I don’t mind doing it one way or

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the other but that is kind of parallel tracks

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so am curious what your thoughts are

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well I guess it’s whatever suits your own needs if you’ve got

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if you’re comfortable using the Web Services I think that’s fine that’s another

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option for you to work in that work flow pipelining environment

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I mean it’s really up to you

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to decide I think it works well but of course if its native inside of the PipelinePilot

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nodes and it works for you then you can avoid getting another call up for

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webservices

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(Questions from the spectators)

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that’s true that’s true and actually he has raised a good the point that

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we always like to take the requests of

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of our users say we want this and in the Pipeline node or we want this on the

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Web Services and we’re going to take that use that as to help prioritize they

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work that we do, thank you!