Hello Colleagues:

We hope you enjoy our last eNews for the year, which contains special offers, info on sponsorship and general items, product news and articles.

Use your budget before the end of the year
Contact us today if you wish to place an order to spend the last of your annual budget. Purchasing additional copies of software, upgrading old copies or registering for training are just some ways to spend the last of your budget before it may be taken away. We are happy to invoice and take your payments this year for orders or training next year.

Trading Hours over the Summer Period
HRS will be closed for the Christmas break from 5pm Thursday, 22 December. We open again for normal business hours of 8.30am to 5pm on Monday, 9 January 2012.

Our support e-mail address support@hrs.co.nz will be monitored through the break. In an emergency please call Ray on 021-1700-713.

Talk to HRS
You can talk to us on our NZ toll free number 0800-477-776 if you wish to discuss any of the products or items mentioned in this newsletter.

Best wishes,

The HRS Team

Special Offers

Special Offer: 90% off CLC Main Workbench for Academics Who Upgrade their Existing Product

Academic researchers can now procure the CLC Main Workbench at a super discounted price of only $US99.

This special upgrade offer saves over 90% off the list price which is around $US985.

Take advantage of this time limited offer before 31 December and receive a perpetual license plus support and updates for the next year.

If you would like to receive future updates and support, you can choose to enter the CLC bio maintenance program once the 12 months are up.

Why invest in the CLC Main Workbench?

The CLC Main Workbench is a comprehensive workbench for advanced DNA, RNA, and protein analyses and is an aggregate of all of the features of CLC bio's Protein, RNA and DNA Workbenches in one integrated software package.

CLC Main Workbench creates a software environment enabling users to make a large number of advanced protein, DNA, and RNA sequence analyses, combined with smooth data management, and excellent graphical viewing and output options and is available on Windows, Mac OS X, and Linux platforms.

To learn more about the CLC Main Workbench, visit www.hrs.co.nz/clcmainworkbench.

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Special Offer: 30% Discount on CLC Genomics Workbench

Purchase the Genomics Workbench before 22 December and receive 30% off.

Commercial Single-user User Discounted Prices (Download Only)
CLC Genomics Workbench - Pay only $9,715 saving 30% (or over $4160 off the list price)

Academic Single-user User Discounted Prices (Download Only)
CLC Genomics Workbench - Pay only $4,860 saving 30% (or over $2080 off the list price)

What is the CLC Genomics Work Bench?

CLC Genomics Workbench helps you analyse and visualise next generation sequencing data. It incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow.

Bruce about this product.

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Special Offer: 10% Discount on All Other CLC Workbenches

Purchase any CLC Workbench before 22 December and receive 10% off.

Commercial Single-user User Discounted Prices (Download Only)
CLC Protein Workbench - Pay only $2,470+gst saving 10%
CLC DNA Workbench* - Pay only $2,470+gst saving 10%
CLC RNA Workbench - Pay only $2,470+gst saving 10%
CLC Main Workbench** - Pay only $4,940+gst saving 10%

Academic Single-user User Discounted Prices (Download Only)
CLC Protein Workbench - Pay only $615+gst saving 10%
CLC DNA Workbench* - Pay only $615+gst saving 10%
CLC RNA Workbench - Pay only $615+gst saving 10%
CLC Main Workbench** - Pay only $1,235+gst saving 10%

About the CLC Work Benches?

CLC Protein Workbench - Advanced Protein Sequence & DNA Analyses
CLC DNA Workbench* - An advanced workbench for DNA analysis
CLC RNA Workbench - An advanced workbench for RNA analysis
CLC Main Workbench** - A comprehensive workbench for advanced DNA, RNA, and protein analyses

Please visit our website for a complete list of features and benefits for each CLC bio workbench at www.hrs.co.nz/prod_list.aspx.

* (formerly Gene WB)
**(formerly Combined WB)

Bruce about these products.

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Special Offer: 20% Discount on ChemOffice Products

Purchase a ChemOffice product before 22 December and receive 20% off.

Commercial Licenses
ChemBioOfficeUltra ---> Now only NZ$4,435+gst with 20% off
ChemOfficeUltra ---> Now only NZ$3,990+gst with 20% off
ChemBioDraw Ultra ---> Now ony NZ$3,100+gst with 20% off
E-Notebook Ultra ---> Now only NZ$1,770+gst with 20% off

Academic Licenses
ChemBioOfficeUltra Academic --> Now only NZ$1,880+gst with 20% off
ChemOfficeUltra Academic --> Now only NZ$1,660+gst with 20% off
ChemBioDraw Ultra Academic --> Now only NZ$1,215+gst with 20% off
E-Notebook Ultra Academic --> Now only NZ$435+gst with 20% off

What is ChemBioOffice?
The ChemBioOffice software suite combines ChemBioDraw, ChemBio3D, ChemFinder, BioViz, BioAssay, Inventory and E-Notebook in the world’s premier desktop suite designed for both chemists and biologists.

What is ChemOffice?
ChemOffice is a powerful suite of software, consisting of ChemDraw, Chem3D, ChemFinder and ChemACX for chemists, BioOffice, BioAssay, BioViz, and BioDraw for biologists, and Inventory, E-Notebook and The Merck Index for scientists. ChemOffice and BioOffice are available for Microsoft Windows.

What is ChemBioDraw?
ChemBioDraw is the sole chemical and biological drawing suite required for the serious life science professional, containing advanced prediction tools and full Web integration using the ChemBioDraw ActiveX/Plugin. Features include proton NMR with peak splitting and highlighting, amino acid and DNA sequence tools, TLC plate drawing tool, Struct=Name, ISIS/Draw mode and stoichiometric analysis.

What is E-Notebook?
Electronically organises information that is typically stored in paper notebooks by incorporating MS Excel & Word, ChemDraw reactions, stoichiometry grids and spectral data.

Bruce to take advantage of this offer or to learn more about the products.

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Sponsorship and General News

HRS Sponsors Our Far South Voyage

HRS is pleased to be a sponsor of the Our Far South Southern Ocean voyage, to take place for 4 weeks from mid-February 2012. Our interest stems from Ray Hoare's student project, where he spent two summer seasons studying the lakes in the dry valleys, and confirming that the reason they were warm was trapped solar heat, rather than volcanism. Ray will return to Antarctica on the voyage and post reports on the company website at www.hrs.co.nz/ourfarsouth.aspx.

The voyage’s goal is to raise New Zealanders' awareness of this beautiful unspoiled environment and the issues that it faces. All members are committed to sharing their adventure with as many people as they can.

Part of this awareness-raising is to involve schools. If you are involved with a local school, please share the following link that explains how schools can get involved:

http://media.gmi.co.nz/Sites/OurFarSouth/mailouts/OFS-Teachers-Newsletter-Template.htm

Visit www.hrs.co.nz/ourfarsouth.aspx for more details and updates from Ray.

Ray if you wish to know more about his involvement in this voyage.

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MATLAB is currently available for use by all staff and students at Otago University

All Otago University staff and students can now use MATLAB on campus and staff have the option to obtain an individual copy of MATLAB for off site academic work.

Here is a list of the products that are available for use campus wide on Otago University’s TAH License:

1. MATLAB 
2. Simulink 
3. Bioinformatics Toolbox 
4. Control System Toolbox 
5. Curve Fitting Toolbox 
6. DSP System Toolbox 
7. Data Acquisition Toolbox 
8. Database Toolbox 
9. Econometrics Toolbox 
10. Financial Derivatives Toolbox 
11. Financial Toolbox 
12. Fixed-Income Toolbox 
13. Fuzzy Logic Toolbox 
14. Image Acquisition Toolbox 
15. Image Processing Toolbox 
16. Instrument Control Toolbox
17. MATLAB Compiler 
18. Mapping Toolbox 
19. Neural Network Toolbox 
20. Optimization Toolbox 
21. Parallel Computing Toolbox 
22. Partial Differential Equation Toolbox 
23. Signal Processing Toolbox 
24. SimMechanics 
25. Simscape 
26. Simulink Control Design 
27. Stateflow 
28. Statistics Toolbox 
29. Symbolic Math Toolbox 
30. System Identification Toolbox 
31. Wavelet Toolbox

To learn more about each of these products, please visit: http://www.mathworks.com/products

Bruce to learn more about a MATLAB TAH license for your institution.

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Register your interest to attend a free MATLAB for Beginners Workshop at the University of Otago in 2012

HRS recently presented a two hour seminar to staff and students at the University of Otago introducing MATLAB and related resources to new and current users. As part of our continued support for Otago, HRS will also present a free hands-on workshop in 2012 to help new users get familiar with MATLAB and jump start their use of the product.

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University of Auckland Student places second in International Simulink Student Challenge

On November 4th, 2011 the first ever Simulink Student Challenge ended. It was a difficult task for the MathWorks to judge the entries and select the 1st, 2nd and 3rd places. The winners of the Simulink Student Challenge were posted to MathWorks.com.  You can learn more about the winners and the entries for the competition at http://www.mathworks.com/academia/student-challenge/

First Place went to Claudio Loconsole from Scuola Superiore Sant'Anna who won $500 for his entry: "Reaching with MATLAB/Simulink."

Second Place went to Jonny Lin from University of Auckland who won US$300 for his entry: "Renewable Energy System for Rural Households."

Third Place went to Jared Frank from Polytechnic Institute of New York University who won $200 for his entry: "iPhone-Controlled Laboratory."

You can view all entries at: http://www.youtube.com/playlist?list=PLFBE7DBBD466439DB

Bruce to be informed about the next Simulink Student Challenge Competition.

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2011 New Zealand Statistics Association Conference Student Prize Results

Congratulations to the winners of the student prizes at the 2011 New Zealand Statistics Association Conference, which were sponsored by Hoare Research Software:

First Place went to Jing Liu from the University of Auckland for his presentation on ‘Diffusion approximation and maximum entropy’.

Second went to Adam Smith from Massey University for his presentation on ‘Linking zeros to abundance in zero-inflated models of species count data’.

Third place was tied between Sam McKechnie from the University of Auckland for his presentation on ‘The potential of life-history models of Coho salmon dynamics’, and Peter Green from the University of Otago for his presentation on ‘Sequential analysis of the Moran Process’.

Please visit the NZSA website to view a complete list of previous winners: http://stats.org.nz/HRS_student_prizes.shtml

Leon about HRS Sponsorship.

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Product News

Maplesoft launches Maple Player for iPad

Technology roadmap lays out future of Maplesoft technology on this platform

Maplesoft recently announced the release of the Maple Player for iPad, an application for the iPad that lets users view and interact with documents created in desktop Maple.  This release is the first step in a plan to increase support for Maplesoft technology on this platform.

The Maple Player for iPad takes advantage of the powerful Maple computation engine, so users can enter values, move sliders, and click buttons to perform calculations and visualise the results.  It comes with a collection of interactive calculators and conceptual explorations.  They can be used to solve arbitrary integrals step-by-step, find derivatives, solve linear systems, plot functions, explore the concept of a limit, and more.  The Maple Player can also display interactive graphical illustrations for approximating the volume of a cylinder, series expansion, and other mathematical concepts. 

This version of the Maple Player provides sample documents that are bundled with the application.  In the next phase, users will be able to access a much wider collection of documents from an online repository. Ultimately, they will be able to use any Maple document on the iPad, whether distributed by Maplesoft, contributed by the Maple community, or authored by themselves.

"The iPad is an increasingly important platform for many of our customers," says Dr. Laurent Bernardin, Executive Vice-President and Chief Scientist at Maplesoft. "The Maple Player can be used to liven up a classroom and provide additional insight to students outside of class. As the technology evolves, we see the Maple Player soon becoming an integral part of the mathematics education experience."

The Maple Player is available for free from the App Store, and can be used by everyone. A copy of desktop Maple is not required to use the Maple Player. 

For more information about Maplesoft’s vision for the iPad, read "Maple and the iPad" by Dr. Laurent Bernardin.

Glen about Maple Products.

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The Top 7 Unique Features of MapleSim

MapleSim is a physical modelling and simulation tool built on a foundation of symbolic computation technology. It efficiently handles all of the complex mathematics involved in the development of engineering models, including multi-domain systems, plant modelling, and control design. MapleSim reduces model development time from months to days while producing high-fidelity, high-performance models.

For more information, visit:
http://www.maplesoft.com/products/maplesim/demo/expandyourmodeling.aspx?P=TC-2255

Glen about MapleSim.

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ChemDraw for Excel

ChemDraw/Excel allows the user to create chemically knowledgeable spreadsheets within the familiar Microsoft Excel environment. You can build and manipulate chemical structures within Excel, compute chemical properties and perform database searches.

Chemically-intelligent Excel spreadsheets are a powerful tool in the day-to-day work of scientists in the pharmaceutical, biotech, and chemical industries. CambridgeSoft has released a new version of ChemDraw/Excel with a new set of features that make it one of the most powerful tools on the market for manipulating chemical lists:

• Add single structures to a spreadsheet from your ChemDraw or E-Notebook programs.
• Import multiple structures, as SDFiles, from online databases such as ChemACX.
• Use ChemDraw’s "Expand Generic Structure" to create a combinatorial library in Excel.
• Automatically determine the IUPAC name of a list of structures.
• Take a list of common names or IUPAC names and convert them into structures with one click.
• Calculate structural and physicochemical properties.
• Perform exact structure, similarity, and substructure searches in a spreadsheet.
• Perform an R-Group analysis on a list of compounds.
• Perform reaction based enumerations.
• And, of course, export all results into standard formats including full interface to a local database in ChemBioFinder.

Bruce to discuss ChemDraw for Excel.

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Product Articles

Free Software?

A lot of people ask Ray why they should buy software when they can get it for free. And his answer is always the same - do you put a value on your time?

An economic analysis of a research or design project should take into account all of the costs involved - designing the project, getting the data, doing the data analysis or algorithm development and publication or passing conclusions on to other people. In most cases the expensive part of the work is the investigator’s time. Obviously, anything that reduces this time reduces the cost of the project, so it is possible to balance the costs of software and training against the time saved.

Most organisations charge the time of their staff at $100 or more dollars per hour, so that any software that reduces the time taken by a couple of days has immediately saved $1000. It is not hard to save many thousands of dollars per year, much more than the cost of the software investment.

Another factor is even more important in many situations - the quality of the work done in the project. Even though free (or, like Excel, virtually free) software may do the basic calculations or analysis, it usually does not have the convenient user interface that ensures you do not ignore important factors, and does not have the on-line help that allows you to use the software correctly. In some case, like MATLAB, the commercial product has pre-programmed, tested routines that you can just pick up and use with confidence, instead of developing your own or getting something from another user who does not fully understand your problem.

You probably spend significant money on a quality phone or computer - maybe the software tools you use need to be regarded in the same way?

Ray if you would like a presentation on one of our products to your company.

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Real-Time Simulation of Physical Systems Using Simscape

View PDF

By Steve Miller and Jeff Wendlandt

Replacing a physical system like a vehicle, plane, or robot with a real-time simulation of a virtual system drastically reduces the cost of testing control software and hardware. In real-time simulation, the inputs and outputs in the virtual world of simulation are read or updated synchronously with the real world. When the simulation time reaches 5, 50, or 500 seconds, exactly the same amount of time has passed in the real world. Testing can take place 24 hours a day, 7 days a week, under conditions that would damage equipment or injure personnel, and it can begin well before physical prototypes are available.

Real-time simulation of physical systems requires finding a combination of model complexity, solver type, solver settings, and simulation hardware that permits execution in real time and delivers results sufficiently close to the results obtained from desktop simulation. Changing these items will often speed up the simulation but reduce the accuracy, or vice-versa. Simscape provides several capabilities that make it easier to configure your models for real-time simulation. This article shows how to configure a Simscape model of a pneumatic actuation system for real-time simulation.

(Figure 1). The steps described apply regardless of the real-time hardware used.

Simscape model of a pneumatic actuation system to be configured for real-time simulation.

Bruce to discuss Simscape

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GPU Programming in MATLAB

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By Jill Reese and Sarah Zaranek

Multicore machines and hyper-threading technology have enabled scientists, engineers, and financial analysts to speed up computationally intensive applications in a variety of disciplines. Today, another type of hardware promises even higher computational performance: the graphics processing unit (GPU).

Originally used to accelerate graphics rendering, GPUs are increasingly applied to scientific calculations. Unlike a traditional CPU, which includes no more than a handful of cores, a GPU has a massively parallel array of integer and floating-point processors, as well as dedicated, high-speed memory. A typical GPU comprises hundreds of these smaller processors (Figure 1).

The greatly increased throughput made possible by a GPU, however, comes at a cost. First, memory access becomes a much more likely bottleneck for your calculations. Data must be sent from the CPU to the GPU before calculation and then retrieved from it afterwards. Because a GPU is attached to the host CPU via the PCI Express bus, the memory access is slower than with a traditional CPU. This means that your overall computational speedup is limited by the amount of data transfer that occurs in your algorithm. Second, programming for GPUs in C or Fortran requires a different mental model and a skill set that can be difficult and time-consuming to acquire. Additionally, you must spend time fine-tuning your code for your specific GPU to optimise your applications for peak performance.

This article demonstrates features in Parallel Computing Toolbox that enable you to run your MATLAB code on a GPU by making a few simple changes to your code. We illustrate this approach by solving a second-order wave equation using spectral methods.

Bruce about MATLAB products.

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Forecasting 101: How to Forecast Data Containing Unusual Demand Periods

Preparing forecasts using data that contains one or more unusually large or small demand periods can be challenging. Depending on your forecasting approach, these "outliers" can have a significant impact on your forecasts. This article surveys three different approaches to forecasting data containing unusual demand periods, discusses the pros and cons of each and makes recommendations about when it is best to use each approach.

To read the full article, visit:
http://www.forecastpro.com/Trends/forecasting101December2011.html

Glen about Forecast Pro.

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CLC bio and BioBase integrate genome

CLC bio and BIOBASE integrate genome informatics framework with Genome Trax databases

At the "NGx: Evolution of Next Generation Sequencing" conference in Providence, Rhode Island, CLC bio and BIOBASE together launched a new plug-in for CLC bio's new framework for visualising, combining and analysing genome data, Genomics Gateway, which integrates the human-curated biological databases contained in BIOBASE's Genome Trax, including TRANSFAC and HGMD Professional.

COO at BIOBASE, Dr. Frank Schacherer, states, "Genomics Gateway from CLC bio is a powerful solution to implement a track-based view of our databases, which not only makes it easy to filter the results, but it also eliminates the need to build your own scripts for this type of work. We're confident researchers will find the combination of an integrated and intuitive solution for advanced analyses combined with expert-curated biological databases, very valuable."

Bioinformatics Specialist at CLC bio, Dr. Anika Joecker, adds, "For example in a re-sequencing workflow, once you have done your mapping, read removal, SNP/DIP detection, and structural variation detection, you're typically looking for the interesting, disease related mutations. This plug-in adds several tracks to a Genomics Gateway trackset, for instance a track for variations found in inherited diseases - the HGMD database - and one track for gene-disease relations. Based on that you can filter your variations to find the ones which are probably causing the disease - simple, yet very efficient!"

Genome Trax license holders will have access to the data in BIOBASE's online databases, including 3,000+ regulatory sites from TRANSFAC, 80,000+ disease-linked mutations from HGMD Professional, 600,000+ ChIP-Seq fragments with best binding site predictions, Post Translational Modifications (PTMs), and Transcription Start Sites (TSSs). The plug-in that integrates these expert-curated biological databases with CLC bio's award-winning platform is free of charge.

CLC bio's Genomics Gateway focuses on comparative filtering of genomic variations, giving scientists a fast and easy way to do functional classification and filtering of SNPs and other kinds of genomic variations, using multiple data sources, including external public databases. This framework offers users convenient and efficient downstream analyses that can easily be combined with existing knowledge.

About BIOBASE
http://www.biobase-international.com/company

About CLC bio
http://www.clcbio.com/about

Bruce about CLC bio products.

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@RISK Article: Using Simulation Statistics Functions

@RISK statistics functions return a desired statistic on simulation results or an input distribution. For example, the function RiskMean(A10) returns the mean of the simulated distribution for the cell A10. These functions are updated real-time as a simulation is running.

@RISK statistics functions include all standard statistics plus percentiles and targets (for example, =RiskPercentile(A10,.99) returns the 99th percentile of the simulated distribution).

@RISK statistics functions can be used the way you would use any standard Excel function. @RISK statistics functions that return a desired statistic on a simulation input distribution have the identifier Theo in the function name. For example, the function RiskTheoMean(A10) returns the mean of the probability distribution in the cell A10.

• Read more about @RISK statistics functions
• Download an example using @RISK statistics functions

Glen about @RISK.

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