Blackberry development

So my blackberry 8330 died a sad death at the best of times, while traveling. It is amazing how much I had come to rely on that device. I use it for online access, tether mode for my laptop, calendar, etc... I went directly to the Verizon store on returning home, and was told the device was hosed, so time to upgrade. The new device is the 9630 World Edition and so far, I am impressed and pleased. That said, I feel a strange need to play with the SDK, or at least get started with the Plazmic CDK.

A quick internet search led me to the blackberry site and their sdk. The link required registration to download but you can find it here. Once you install the base application, you need to run the update as well.

Once I get the install finished and see how it works, I will update with a new post. In the meantime, keep your fingers crossed on the install since I am running Windows 7 and it is not listed as supported - probably due in part to the fact that Windows 7 has not been generally released yet.

cross posted from my digital vision site as well.

UI Mockup

Recently, a friend of mine showed me a great UI mockup tool he has been using for application development with his team. The tool is called Balsamiq Mockups and it allows for simple UI design and discussion in a line drawing manner without all the line drawing. The added benefit is that the client is not led to believe there is working code behind a prototype mockup as is often the case with a simple forms construct.

Mounting Virtual Drives in Vista

As a long time MSDN subscriber, I regularly pull down iso files for installations on one or another of my machines - though maybe less regularly now then previously as evidenced by the fact that I just hit this particular wall on my vista desktop. Using the VCD utility and mounting the driver JIT worked great until I tried it on my vista box, where it would not load the driver. Rather then spend too much time working on a deep level solution, I turned to the net as I have deadlines to meet :)

I was happy to find a new and also free solution that works even better in Virtual Clone Drive.

Happily after install, it works like a charm and maked iso use very simple with a file association.

Budapest

The conference went well and I got a solid response on my talk. The morning talks all pointed toward foundational needs for deploying these solutions and set up the discussion quite well.

Today, I caught a talk from Nico Adams, of Cambridge University, regarding the Semantic Web. It was a good talk and what really got me was that this was a follow on to a great talk by Randy Julian, CEO of Indigo BioSystems, at the AAPS earlier in the week on a very similar note, and also followed on the meeting I had with Jim Karkanias at Microsoft regarding their information strategy and the thinking behind the Amalga platform. While they are all on different paths, they are headed in similar directions and the thinking trend is toward data management at the atomic level. I am looking forward to seeing where this goes.

AAPS - Update from Seattle

The speakers dinner last night was enjoyable and informative. The challenges coming out of the ligand binding labs are the same as those faced by the rest of my clients and center around key information exchange challenges.

As a deliverable set from yesterday, the group discussed several key focus areas, several of which resonated with me.

Data exchange was a hot topic with a desire for standardized information exchange so systems could talk to each other with minimal work. There is already work in the industry on this topic and I pointed to several of the current and emerging transport standards.

Instrument and software validation and the easing of the process was a highly debated topic as it represents so much of an impact for the GLP labs. The options and discussion ranged from validation accelerator packs to FDA recognized validation standards that allow a vendor to certify, reducing the customer level validation to the 20% or less of customization or configuration.

Also discussed was the desire to have a standardized "plug and play" infrastructure for instrument hardware. This spurred a number of discussions around the implications, not the least of which is the need to implement bidirectional communication in the hardware and software layers of the instruments to make this possible. The lack of common standards to build to and a governing body to work with makes this all the more challenging. My suggestion to the group was to not take on this as an outcome, but rather take on a paper with requirements and standards recommendations, that can then be used as a foundation for discussion with the key players. We need to get on the same page with respect to what it means to have integration at the hardware and driver level before we can get to the level of discussing implementation in detail.

All in all, it was good discussion and I am looking forward to my session later today, discussing the ELN and LIMS roles in these and other areas.

Traveling...

Philly to Seattle, Speak at a conference, meet with people. Seattle to Frankfurt, Frankfurt to Budapest. Speak at a conference, meet with people and see the city. Budapest to Frankfurt and Frankfurt to Philly - home again. A lot of time in the air is in my future this month!

Ontology Lookup Service

Who knew - Sourceforge supports an Ontology lookup service! Check it out here: http://www.ebi.ac.uk/ontology-lookup/

I have to dig a little more to see if there is a publicly accessible API we can hit for this - sort of like encoding a-la MEDRA.

LinkedIn Profile for Jim King

LinkedIn profile

I have been playing around with LinkedIn and looking at their API. I found a widget that provides a snapshot of my linkedIn profile so I am including it here. For those of you not in the know on LinkedIn, it is a business networking site.

Microsoft – the integration story

Working in IT, I run into people with religious convictions all the time - software religion that is. It amazes me how often people fall into one or the other camp and are completely blinded by the "right thing" in their mind. This most often occurs with the Microsoft, Open Source, and Java camps for techs and Microsoft and Mac for many end users.

While all platforms have strengths and weaknesses, no one platform is the best fit for all use, and we should be focused more on interoperability than on justifying a platform choice.

As for Microsoft, in the enterprise it is a hard sell to unseat the giant. They own the desktop and that makes the stack so much more compelling. While any single product can likely be beat by a best of breed comparison, their greatest strength comes in their integration story. So... what's the big deal? let it be while others work on a similar story and accept that this is reality for now. Learn to work with it and let's figure out how to make our Linux and Mac machines work in this environment while alternatives are created. Collaboration is the only way to create a new stack option for seamless integration.

A simple thank you

I am wrapping up a significant project at work and I had the support of 3 admins to manage scheduling and logistics as we had a rather grueling pace for a while. I wanted to thank them with a small gift and a note, but not being the best at the soft communications, I did a quick google for thank you note tips - this one hit the spot and sounded like good general advice.

Ontology based data & semantic relationships

Working through a data architecture and strategy for clients recently, I had to compile some information regarding development of the landscape. This information is reflected below.

The primary components to reference are detailed in the included diagram. In this case, the ontology is clearly a piece of the stack, but not the “data” or the single UI.

The ontology is best thought of as a view of an established information set that uses concepts to define relationship. The data is then mapped onto ontology to provide a specific high value view of the data, aiding in the generation of information and knowledge. Clearly there is an assumption that as a precursor to the use of the selected ontology, significant work has gone into the process of cleaning the target data through direct manipulation or a meta data based transformation layer to manage synonym matching, etc. across sources.

Another definition, more succinct is, “Ontologies are computable conceptualisations of a knowledge domain” as defined by Nico Adams, emphasizing the transformation from data to information that can then be further acted upon.

The OWL Web Ontology Language is designed for use by applications that need to process the content of information instead of just presenting information to humans. OWL facilitates greater machine interpretability of Web content than that supported by XML, RDF, and RDF Schema (RDF-S) by providing additional vocabulary along with a formal semantics. OWL has three increasingly-expressive sublanguages: OWL Lite, OWL DL, and OWL Full. Source: http://www.w3.org/TR/owl-features/

The semantic layer-cake.: (Copyright © 2008 World Wide Web Consortium, (Massachusetts Institute of Technology, European Research Consortium for Informatics and Mathematics, Keio University). All Rights Reserved. http://www.w3.org/Consortium/Legal

Useful links :

1. W3 OWL Reference a) http://www.w3.org/TR/owl-features/
2. Good article on Ontology implementation a) http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T64-4GMB0F0-F&_user=358874&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000017638&_version=1&_urlVersion=0&_userid=358874&md5=4b5c6decc4b2f01fad8183b00aec72b1
3. 3) DDI - An Ontology for Drug Discovery Investigations a) http://users.aber.ac.uk/ddq/ddi/wiki/index.php?title=Main_Page
4. Open BioMedical Ontologies a) http://www.obofoundry.org/crit.shtml
5. OWL ontology browser a) http://pellet.owldl.com/ontology-browser/
6. OBO Ontology Download Matrix a) http://www.berkeleybop.org/ontologies/
7. Semantic Chemistry a) http://www.semanticuniverse.com/articles-semantic-chemistry.html

Reference:Stephen P. Gardner, Ontologies and semantic data integration, Drug Discovery Today, Volume 10, Issue 14, 15 July 2005, Pages 1001-1007, ISSN 1359-6446, DOI: 10.1016/S1359-6446(05)03504-X.(http://www.sciencedirect.com/science/article/B6T64-4GMB0F0-F/2/f296f93f44347cfd561668ede72ac5f9)

Nico Adams, Semantic Chemistry http://www.semanticuniverse.com/articles-semantic-chemistry.html

More to come...

Plethora of web links

Another good find: http://www.alvit.de/handbook/

This is a page with links to all sorts of web content and developer tools and widgets. Enjoy

MS Office "Save as PDF"

If you use Microsoft Office 2007, you need this add-in: Microsoft Save as PDF or XPS

This download allows you to export and save to the PDF and XPS formats in eight 2007 Microsoft Office programs. It also allows you to send as e-mail attachment in the PDF and XPS formats in a subset of these programs. It was a part of the standard functionality until Adobe got a little tweaked with Microsoft stepping on their toes. Even with it a separate download, it's still pretty painless except the Windows Genuine Annoyance confirmation.

Get it now

Microsofts open source projects

While attending the HLS Devcon today, I heard one of the sweetest sounds I have yet heard from a Microsoft conference... In a session on Ajax, the presenter spoke about the technology, what it could do and how it worked. Then came the punchline... by the way, it works with PHP, Java, on Apache, whatever you want. Not the party line about the language of your choice being available in the VS IDE, rather this was talking about using a Microsoft technology to help devs build their php sites. Well done Microsoft.

Also a topic of conversation was the codeplex resource. This is a Microsoft repository for open source projects. In their own words, "CodePlex is Microsoft's open source project hosting web site. You can use CodePlex to create new projects to share with the world, join others who have already started their own projects, or use the applications on this site and provide feedback."