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Science Code Manifesto

Making sure the code used to perform an analysis is available has become an imperative in data (and software) intensive science. We believe that the entire provenance of an analysis should be available and are proud to endorse the Science Code Manifesto as an important step towards this goal.

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Ovation 1.1.2

Ovation 1.1.2 is now available for download. Read the release notes at http://bit.ly/AvZACm.  This release brings support for URL-referenced Response and Resource data, AnalysisRecord hiearchies and many performance improvements and bug fixes.

We’re especially proud of the AnalysisRecord hierarchy representation. It’s now possible to represent complex analysis pipelines in Ovation’s database. Even analyses that feed multiple down-stream analyses can be easily represented, tracked and shared.

This upgrade is recommended for all users. Current customers can download the latest versions from download.physionconsulting.com. If you are interested in hearing more about Ovation or receiving a demo license, please let us know (info@physionconsulting.com).

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Ovation 1.1

Ovation 1.1 is now available. This release brings great annotation and collaboration features. This release also has several significant performance improvements, especially for users on slow networks.

We’re very proud of the new annotation features, which enhance the ability of many users to annotate the same dataset. Long after data is collected and analyzed these rich interpretations added by many users over the lifetime of the data will bring new value to old data sets. Instead of trying to guess what the original researcher thought of the data, imagine being able to read their annotations directly out of the database. Of course, you’ll be able to add your own as well. And you can now search for data based on these annotations and interpretations. So, for example, this release allows behavioral researchers to find trials in the database where more than one user annotated a behavior on video but the annotated regions do not (or do) overlap in space.

Performance enhancements in this release greatly reduce the amount of data that Ovation transmits over the network between server and client. On slower networks such as VPNs, this release brings fifty-fold speed gains in our testing.

Check out the release notes, or download the installer.

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Ovation: data management for the biological sciences

I’d like to invite you to take a look at our new whitepaper describing the features of Ovation for the biological sciences.

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Ovation 1.0.4

Ovation 1.0.4 is now available. This release brings new collaboration features, performance enhancements and full feature parity for Windows platforms (XP, Vista and Windows 7). Because of a schema change in this release, users should upgrade all clients simultaneously; after the upgrade, older clients will not be able to edit or query collaborative annotations such as keywords and properties.

Existing Ovation users can download the 1.0.4 installers from download.physionconsulting.com. If you are interested in trying Ovation, please call us (617-299-9520) or send an email to info@physionconsulting.com. We’d be happy to set you up with a trial version of Ovation.

Ovation 1.0.3

Ovation 1.0.3 is now available. This release brings explicit sample rate support for Response objects as well as several minor bug fixes and API improvements. Because of a schema change in this release, users should upgrade all clients simultaneously; after the upgrade, older clients will not be able to connect to an upgraded database.

Existing Ovation users can download the 1.0.3 installers from download.physionconsulting.com. If you are interested in trying Ovation, please call us (617-299-9520) or send an email to info@physionconsulting.com. We’d be happy to set you up with a trial version of Ovation.

Several new and exciting features are coming in the next few weeks, so stay tuned!

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Flat vs. Hierarchical User Interface Models

Apple recently introduced OS X “Lion“, with several new user interface elements and paradigms borrowed from the iOS operating system that powers the iPhone and iPad. One of the features that has generated the significant negative reaction from user interface blogs has been Launchpad. Launchpad looks very similar to  the iOS app launcher, with a 2-D grid of application icons and folders. Several user interface experts have commented that this 2-D icon grid is a step “back” from more complex user interface paradigms for application organization and browsing.

At Physion Consulting, we’ve thought a lot about how to make browsing and organizing collections easier. In this case, I believe that Launchpad’s UI is actually a good idea. The issue is, fundamentally, whether flat or hierarchical organization is easier for a user.

Scientists (and software developers) tend to think in hierarchical organization models. Human working memory is often described as “7 ± 2″ items. In other words, classical psychophysics teaches us that we can keep about seven “things” in working memory at a time. This number of course varies with the task, the experience of the user with the task and many other factors, but the general principle stands. In a world with too many “things”, the human solution is often to categorize them to reduce the number of pieces of information needed at a time. When the number of categories gets large, we create categories of categories, etc.

Categories and categories of categories do not necessarily reflect the organization of the world. Rather they are a crutch to help humans reason about large groups of things. In the real world, relationships cut across category boundaries (files relate to more than one project, species may have more than one ancestor, etc.), making hierarchical organiation restrictive. Even when relationships are well modeled by hierarchy, finding existing data then requires the user to remember where in the hierarchy the data resides. If you’ve ever used Spotlight (or desktop search of your choice) or a Desktop full of files rather than searching through the nested folders on your hard drive, you’ve experienced the downside of hierarchical organization.

In this age of computer-aided workflows, why are we stuck with hierarchical systems? Why can’t we delegate some of the organization to the computer? If the operating system can keep track of apps we use frequently, files belonging to projects etc. (and it can), why don’t we let it present a flat, simple representation of those groups?

In Ovation, we take a similar approach. We let you view data in any arbitrary hierarchy, but we also let you view the flat list of data that matches a query. As you refine and change the query, the list of matchin items updates automatically. Thus, rather than thinking of where your data sits in a hierarcy of folders, you can think about what data you want and let Ovation collect it from the database for you.

 

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Ovation 1.0

We shipped Ovation 1.0 on April 12th! Ovation is a revolutionary scientific data management system designed for modern, data-intensive science. A beta tester said that “it’s like iTunes for scientific data.” If your data is still living in the days of “MP3s in folders”, come have a look at Ovation.

Our team would be happy to talk with you about how Ovation can help you or your lab manage, query, explore and share your data more effectively. Drop us a line at info@physionconsulting.com.

Do you want to help change the face of basic science?

We’re hiring new software engineers for our technical staff. Maybe you’re the person we’re looking for.

About us

Physion Consulting is hiring full time developers in the Cambridge, MA area. We’re a profitable, boot-strapped startup developing revolutionary data management software for the scientific research community. We are the first successful entrant in a $21B market and expect to lead development of this exciting new field.

We care about our developers, offer competitive pay, full medical & dental benefits and a great work environment. We’ll gladly help you set up an internship

Who we’re looking for

You’re a highly motivated, awesome programmer with excellent engineering, math and science skills and a demonstrated ability to ship software. You enjoy working on products that revolutionize the scientific world. You have a life-long appetite for learning and are comfortable in many programming languages and paradigms, operating systems, and development environments. You enjoy difficult technical challenges and are comfortable working through the entire lifecycle of product development from conception to production.

Your Skills

• 5+ years of application oriented software development experience on Mac and Windows
• 5+ years of C++, Java, C# and/or Python programming
• Comfort with at least one functional programming language
• Excellent communication and customer relation skills
• Experience with algorithm design and analysis
• Experience with Object Database Management Systems preferred
• Experience with Cocoa or WPF highly preferred
• Bachelors degree in Computer Science or related field required, Masters degree preferred

Joel Test score: 11/12

If you’re interested, please send us a link to your StackOverflow account, blog, GitHub or Bitbucket accounts at jobs@physionconsulting.com. If all else fails, we’ll take a look at a resume too.

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Unit testing Arduino interaction code from Python

An other useful snippet from Todd Stavish from our Arduino data acquisition project: this sample code shows how to upload new hex images to an Arduino controller. We’re using this technique to unit test our host application’s interaction with the Arduino controller. By using specific hex images for each test, we can focus on a particular piece of the host-Arduino system for each test, making the tests smaller, easier to debug and less fragile.