JMP Genomics 5 released

Animation of the structure of a section of DNA...
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Close to the launch of JMP9 with it’s R integration comes the announcement of JMP Genomics 5 released. The product brief is available here http://jmp.com/software/genomics/pdf/103112_jmpg5_prodbrief.pdf and it has an interesting mix of features. If you want to try out the features you can see http://jmp.com/software/license.shtml

As per me, I snagged some “new”stuff in this release-

  • Perform enrichment analysis using functional information from Ingenuity Pathways Analysis.+
  • New bar chart track allows summarization of reads or intensities.
  • New color map track displays heat plots of information for individual subjects.
  • Use a variety of continuous measures for summarization.
  • Using a common identifier, compare list membership for up tofive groups and display overlaps with Venn diagrams.
  • Filter or shade segments by mean intensity, with an optionto display segment mean intensity and set a reference valuefor shading.
  • Adjust intensities or counts for experimental samples using paired or grouped control samples.
  • Screen paired DNA and RNA intensities for allele-specific expression.
  • Standardize using a shifting factor and perform log2transformation after standardization.
  • Use kernel density information in loess and quantile normalization.
  • Depict partition tree information graphically for standard models with new Tree Viewer
  • Predictive modeling for survival analysis with Harrell’s assessment method and integration with Cross-Validation Model Comparison.

That’s right- that is incorporating the work of our favorite professor from R Project himself- http://biostat.mc.vanderbilt.edu/wiki/Main/FrankHarrell

Apparently Prof Frank E was quite a SAS coder himself (see http://biostat.mc.vanderbilt.edu/wiki/Main/SasMacros)

Back to JMP Genomics 5-

The JMP software platform provides:

• New integration capabilities let R users leverage JMP’s interactivegraphics to display analytic results.

• Tools for R programmers to build and package user interfaces that let them share customized R analytics with a broader audience.•

A new add-in infrastructure that simplifies the integration of external analytics into JMP.

 

+ For people in life sciences who like new stats software you can also download a trial version of IPA here at http://www.ingenuity.com/products/IPA/Free-Trial-Software.html

John Sall sets JMP 9 free to tango with R

 

Diagnostic graphs produced by plot.lm() functi...
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John Sall, founder SAS AND JMP , has released the latest blockbuster edition of flagship of JMP 9 (JMP Stands for John’s Macintosh Program).

To kill all birds with one software, it is integrated with R and SAS, and the brochure frankly lists all the qualities. Why am I excited for JMP 9 integration with R and with SAS- well it integrates bigger datasets manipulation (thanks to SAS) with R’s superb library of statistical packages and a great statistical GUI (JMP). This makes JMP the latest software apart from SAS/IML, Rapid Miner,Knime, Oracle Data Miner to showcase it’s R integration (without getting into the GPL compliance need for showing source code– it does not ship R- and advises you to just freely download R). I am sure Peter Dalgaard, and Frankie Harell are all overjoyed that R Base and Hmisc packages would be used by fellow statisticians  and students for JMP- which after all is made in the neighborhood state of North Carolina.

Best of all a JMP 30 day trial is free- so no money lost if you download JMP 9 (and no they dont ask for your credit card number, or do they- but they do have a huuuuuuge form to register before you download. Still JMP 9 the software itself is more thoughtfully designed than the email-prospect-leads-form and the extra functionality in the free 30 day trial is worth it.

Also see “New Features  in JMP 9  http://www.jmp.com/software/jmp9/pdf/new_features.pdf

which has this regarding R.

Working with R

R is a programming language and software environment for statistical computing and graphics. JMP now  supports a set of JSL functions to access R. The JSL functions provide the following options:

• open and close a connection between JMP and R

• exchange data between JMP and R

•submit R code for execution

•display graphics produced by R

JMP and R each have their own sets of computational methods.

R has some methods that JMP does not have. Using JSL functions, you can connect to R and use these R computational methods from within JMP.

Textual output and error messages from R appear in the log window.R must be installed on the same computer as JMP.

JMP is not distributed with a copy of R. You can download R from the Comprehensive R Archive Network Web site:http://cran.r-project.org

Because JMP is supported as both a 32-bit and a 64-bit Windows application, you must install the corresponding 32-bit or 64-bit version of R.

For details, see the Scripting Guide book.

and the download trial page ( search optimized URL) –

http://www.sas.com/apps/demosdownloads/jmptrial9_PROD__sysdep.jsp?packageID=000717&jmpflag=Y

In related news (Richest man in North Carolina also ranks nationally(charlotte.news14.com) , Jim Goodnight is now just as rich as Mark Zuckenberg, creator of Facebook-

though probably they are not creating a movie on Jim yet (imagine a movie titled “The Statistical Software” -not just the same dude feel as “The Social Network”)

See John’s latest interview :

The People Behind the Software: John Sall

http://blogs.sas.com/jmp/index.php?/archives/352-The-People-Behind-the-Software-John-Sall.html

Interview John Sall Founder JMP/SAS Institute

https://decisionstats.com/2009/07/28/interview-john-sall-jmp/

SAS Early Days

https://decisionstats.com/2010/06/02/sas-early-days/

Which software do we buy? -It depends

Software (novel)
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Often I am asked by clients, friends and industry colleagues on the suitability or unsuitability of particular software for analytical needs.  My answer is mostly-

It depends on-

1) Cost of Type 1 error in purchase decision versus Type 2 error in Purchase Decision. (forgive me if I mix up Type 1 with Type 2 error- I do have some weird childhood learning disabilities which crop up now and then)

Here I define Type 1 error as paying more for a software when there were equivalent functionalities available at lower price, or buying components you do need , like SPSS Trends (when only SPSS Base is required) or SAS ETS, when only SAS/Stat would do.

The first kind is of course due to the presence of free tools with GUI like R, R Commander and Deducer (Rattle does have a 500$ commercial version).

The emergence of software vendors like WPS (for SAS language aficionados) which offer similar functionality as Base SAS, as well as the increasing convergence of business analytics (read predictive analytics), business intelligence (read reporting) has led to somewhat brand clutter in which all softwares promise to do everything at all different prices- though they all have specific strengths and weakness. To add to this, there are comparatively fewer business analytics independent analysts than say independent business intelligence analysts.

2) Type 2 Error- In this case the opportunity cost of delayed projects, business models , or lower accuracy – consequences of buying a lower priced software which had lesser functionality than you required.

To compound the magnitude of error 2, you are probably in some kind of vendor lock-in, your software budget is over because of buying too much or inappropriate software and hardware, and still you could do with some added help in business analytics. The fear of making a business critical error is a substantial reason why open source software have to work harder at proving them competent. This is because writing great software is not enough, we need great marketing to sell it, and great customer support to sustain it.

As Business Decisions are decisions made in the constraints of time, information and money- I will try to create a software purchase matrix based on my knowledge of known softwares (and unknown strengths and weakness), pricing (versus budgets), and ranges of data handling. I will add in basically an optimum approach based on known constraints, and add in flexibility for unknown operational constraints.

I will restrain this matrix to analytics software, though you could certainly extend it to other classes of enterprise software including big data databases, infrastructure and computing.

Noted Assumptions- 1) I am vendor neutral and do not suffer from subjective bias or affection for particular software (based on conferences, books, relationships,consulting etc)

2) All software have bugs so all need customer support.

3) All software have particular advantages , strengths and weakness in terms of functionality.

4) Cost includes total cost of ownership and opportunity cost of business analytics enabled decision.

5) All software marketing people will praise their own software- sometimes over-selling and mis-selling product bundles.

Software compared are SPSS, KXEN, R,SAS, WPS, Revolution R, SQL Server,  and various flavors and sub components within this. Optimized approach will include parallel programming, cloud computing, hardware costs, and dependent software costs.

To be continued-

 

 

 

 

Windows Azure vs Amazon EC2 (and Google Storage)

Here is a comparison of Windows Azure instances vs Amazon compute instances

Compute Instance Sizes:

Developers have the ability to choose the size of VMs to run their application based on the applications resource requirements. Windows Azure compute instances come in four unique sizes to enable complex applications and workloads.

Compute Instance Size CPU Memory Instance Storage I/O Performance
Small 1.6 GHz 1.75 GB 225 GB Moderate
Medium 2 x 1.6 GHz 3.5 GB 490 GB High
Large 4 x 1.6 GHz 7 GB 1,000 GB High
Extra large 8 x 1.6 GHz 14 GB 2,040 GB High

Standard Rates:

Windows Azure

  • Compute
    • Small instance (default): $0.12 per hour
    • Medium instance: $0.24 per hour
    • Large instance: $0.48 per hour
    • Extra large instance: $0.96 per hour
  • Storage
    • $0.15 per GB stored per month
    • $0.01 per 10,000 storage transactions
  • Content Delivery Network (CDN)
    • $0.15 per GB for data transfers from European and North American locations*
    • $0.20 per GB for data transfers from other locations*
    • $0.01 per 10,000 transactions*

Source –

http://www.microsoft.com/windowsazure/offers/popup/popup.aspx?lang=en&locale=en-US&offer=MS-AZR-0001P

and

http://www.microsoft.com/windowsazure/windowsazure/

Amazon EC2 has more options though——————————-

http://aws.amazon.com/ec2/pricing/

Standard On-Demand Instances Linux/UNIX Usage Windows Usage
Small (Default) $0.085 per hour $0.12 per hour
Large $0.34 per hour $0.48 per hour
Extra Large $0.68 per hour $0.96 per hour
Micro On-Demand Instances Linux/UNIX Usage Windows Usage
Micro $0.02 per hour $0.03 per hour
High-Memory On-Demand Instances
Extra Large $0.50 per hour $0.62 per hour
Double Extra Large $1.00 per hour $1.24 per hour
Quadruple Extra Large $2.00 per hour $2.48 per hour
High-CPU On-Demand Instances
Medium $0.17 per hour $0.29 per hour
Extra Large $0.68 per hour $1.16 per hour
Cluster Compute Instances
Quadruple Extra Large $1.60 per hour N/A*
* Windows is not currently available for Cluster Compute Instances.

http://aws.amazon.com/ec2/instance-types/

Standard Instances

Instances of this family are well suited for most applications.

Small Instance – default*

1.7 GB memory
1 EC2 Compute Unit (1 virtual core with 1 EC2 Compute Unit)
160 GB instance storage (150 GB plus 10 GB root partition)
32-bit platform
I/O Performance: Moderate
API name: m1.small

Large Instance

7.5 GB memory
4 EC2 Compute Units (2 virtual cores with 2 EC2 Compute Units each)
850 GB instance storage (2×420 GB plus 10 GB root partition)
64-bit platform
I/O Performance: High
API name: m1.large

Extra Large Instance

15 GB memory
8 EC2 Compute Units (4 virtual cores with 2 EC2 Compute Units each)
1,690 GB instance storage (4×420 GB plus 10 GB root partition)
64-bit platform
I/O Performance: High
API name: m1.xlarge

Micro Instances

Instances of this family provide a small amount of consistent CPU resources and allow you to burst CPUcapacity when additional cycles are available. They are well suited for lower throughput applications and web sites that consume significant compute cycles periodically.

Micro Instance

613 MB memory
Up to 2 EC2 Compute Units (for short periodic bursts)
EBS storage only
32-bit or 64-bit platform
I/O Performance: Low
API name: t1.micro

High-Memory Instances

Instances of this family offer large memory sizes for high throughput applications, including database and memory caching applications.

High-Memory Extra Large Instance

17.1 GB of memory
6.5 EC2 Compute Units (2 virtual cores with 3.25 EC2 Compute Units each)
420 GB of instance storage
64-bit platform
I/O Performance: Moderate
API name: m2.xlarge

High-Memory Double Extra Large Instance

34.2 GB of memory
13 EC2 Compute Units (4 virtual cores with 3.25 EC2 Compute Units each)
850 GB of instance storage
64-bit platform
I/O Performance: High
API name: m2.2xlarge

High-Memory Quadruple Extra Large Instance

68.4 GB of memory
26 EC2 Compute Units (8 virtual cores with 3.25 EC2 Compute Units each)
1690 GB of instance storage
64-bit platform
I/O Performance: High
API name: m2.4xlarge

High-CPU Instances

Instances of this family have proportionally more CPU resources than memory (RAM) and are well suited for compute-intensive applications.

High-CPU Medium Instance

1.7 GB of memory
5 EC2 Compute Units (2 virtual cores with 2.5 EC2 Compute Units each)
350 GB of instance storage
32-bit platform
I/O Performance: Moderate
API name: c1.medium

High-CPU Extra Large Instance

7 GB of memory
20 EC2 Compute Units (8 virtual cores with 2.5 EC2 Compute Units each)
1690 GB of instance storage
64-bit platform
I/O Performance: High
API name: c1.xlarge

Cluster Compute Instances

Instances of this family provide proportionally high CPU resources with increased network performance and are well suited for High Performance Compute (HPC) applications and other demanding network-bound applications. Learn more about use of this instance type for HPC applications.

Cluster Compute Quadruple Extra Large Instance

23 GB of memory
33.5 EC2 Compute Units (2 x Intel Xeon X5570, quad-core “Nehalem” architecture)
1690 GB of instance storage
64-bit platform
I/O Performance: Very High (10 Gigabit Ethernet)
API name: cc1.4xlarge

Also http://www.microsoft.com/en-us/sqlazure/default.aspx

offers SQL Databases as a service with a free trial offer

If you are into .Net /SQL big time or too dependent on MS, Azure is a nice option to EC2 http://www.microsoft.com/windowsazure/offers/popup/popup.aspx?lang=en&locale=en-US&offer=COMPARE_PUBLIC

Updated- I just got approved for Google Storage so am adding their info- though they are in Preview (and its free right now) 🙂

https://code.google.com/apis/storage/docs/overview.html

Functionality

Google Storage for Developers offers a rich set of features and capabilities:

Basic Operations

  • Store and access data from anywhere on the Internet.
  • Range-gets for large objects.
  • Manage metadata.

Security and Sharing

  • User authentication using secret keys or Google account.
  • Authenticated downloads from a web browser for Google account holders.
  • Secure access using SSL.
  • Easy, powerful sharing and collaboration via ACLs for individuals and groups.

Performance and scalability

  • Up to 100 gigabytes per object and 1,000 buckets per account during the preview.
  • Strong data consistency—read-after-write consistency for all upload and delete operations.
  • Namespace for your domain—only you can create bucket URIs containing your domain name.
  • Data replicated in multiple data centers across the U.S. and within the same data center.

Tools

  • Web-based storage manager.
  • GSUtil, an open source command line tool.
  • Compatible with many existing cloud storage tools and libraries.

Read the Getting Started Guide to learn more about the service.

Note: Google Storage for Developers does not support Google Apps accounts that use your company domain name at this time.

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Pricing

Google Storage for Developers pricing is based on usage.

  • Storage—$0.17/gigabyte/month
  • Network
    • Upload data to Google
      • $0.10/gigabyte
    • Download data from Google
      • $0.15/gigabyte for Americas and EMEA
      • $0.30/gigabyte for Asia-Pacific
  • Requests
    • PUT, POST, LIST—$0.01 per 1,000 requests
    • GET, HEAD—$0.01 per 10,000 requests

Jump to JMP: Using Data Analysis in a visual manner

Over the past month or so, I have really begun to appreciate the GUI of JMP. It is very clean and intutively designed. And excellent for a SAS Environment .

Best of all you can easily download a 30 day trial and pricing for this software is quite reasonable.

The worst part of JMP- the droll website. In fact on website, I can deduce something of an Ohri’s Law on Websites.

The better the software, the worse off is the website.

Corollary- The worse off the software, the better is the website in terms of glitz.

JMP is definitely worth a trial for 30 days if you

a) Want to learn a new stats software skill fast

2) Unhappy with visual data analysis of current softwares.

Integrating JMP ‘s functionality with a BI reporting tool is a formidable data decisionmaking tool and it works nicely for me in data analysis I do.

http://www.sas.com/apps/demosdownloads/jmptrial8_PROD__sysdep.jsp?packageID=000503&jmpflag=Y

jmp