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About Jeff Masters
Cat 6 lead authors: WU cofounder Dr. Jeff Masters (right), who flew w/NOAA Hurricane Hunters 1986-1990, & WU meteorologist Bob Henson, @bhensonweather
By: Dr. Jeff Masters , 2:38 PM GMT on May 24, 2012
An area of disturbed weather (Invest 94L) over South Florida, Cuba, the Bahamas, and the Western Caribbean is bringing gusty winds heavy rains to the region, and is headed north-northeast along the east coast of Florida. Miami is under an areal flood watch today for rains of 1 - 3 inches, and rains in excess of one inch have already fallen over Key Largo today. The disturbance is generating some impressive winds this morning along the Southeast Florida coast--Fowey Rocks recorded sustained southeast winds of 33 mph at 10am EDT, and Molasses Reef on Key Largo had 31 mph sustained winds. The disturbance is under a very high 40 - 50 knots of wind shear, according that the latest SHIPS model analysis, making development very unlikely today. As 94L slides north-northeast along the coast on Friday and Saturday, wind shear is expected to decrease, and several of our reliable models predict that 94L could organize into a subtropical depression on Saturday or Sunday off the coast of North Carolina/South Carolina. NHC is giving 94L a 20% chance of developing by Saturday morning. A ridge of high pressure is expected to build in over the weekend off the East Coast, which will force 94L to the southwest back towards the coast. Heavy rains from 94L are likely to begin affecting coastal South Carolina, Georgia, and Northern Florida on Saturday and Sunday. If these rains do materialize, they would be welcome, considering the moderate to severe drought conditions in the area.
Figure 1. Morning radar image of heavy rains from Invest 94L affecting Southeast Florida.
Hurricane Bud heads towards Mexico
Hurricane Bud finally took advantage of its favorable environment of low wind shear and warm ocean temperatures and became a Category 2 hurricane this morning. Recent satellite loops show a well-organized storm with a prominent eye, cold eyewall cloud tops, and good low-level spiral banding. It is possible that Bud could attain Category 3 status later today. An Air Force hurricane hunter aircraft will investigate Bud this afternoon to gauge Bud's strength. Hurricanes are uncommon in the Eastern Pacific in May; there have been just twelve since record keeping began in 1949--an average of one May hurricane every five years. The earliest Eastern Pacific hurricane was Hurricane Alma of 1990, which became a hurricane on May 15. There have been only two major Category 3 or stronger May hurricanes. Here is a list of the twelve May hurricanes in the Eastern Pacific:
Hurricane Bud of 2012
Hurricane Adrian of 2005
Hurricane Alma of 2002 (major)
Hurricane Adolph of 2001 (major)
Hurricane Aletta of 2000
Hurricane Alma of 1990
Hurricane Agatha of 1986
Hurricane Adolph of 1983
Hurricane Aletta of 1978
Hurricane Agatha of 1971
Hurricane Adelle of 1970
Unnamed Hurricane of 1956
Figure 2. Morning satellite image of Bud.
Forecast for Bud
Bud will continue towards the coast of Mexico the next two days, pulled northwards by a trough of low pressure moving across the U.S. This trough will lift out and a ridge of high pressure will build in its place, and most of the computer models predict Bud will stall just offshore--or get pulled apart so that its low level center stays offshore, and its mid-level center moves inland. NHC is currently basing its track forecast on the ECMWF and GFS models, which were the two best performing models in both 2010 and 2011. An outer spiral band of Bud is already bringing a few heavy rain showers to the coast of Mexico near Manzanillo, and rains will increase in intensity on Friday and Saturday. The hurricane is expected to encounter more hostile condition--dry air, cooler SSTs, and higher wind shear--that will weaken the storm on Friday and Saturday. This should decrease the winds enough so that heavy rain will be the main threat from Bud. The coast where Bud is headed towards is very mountainous, and flash floods and dangerous mudslides will be a concern there. The region was not under drought conditions as of the end of April, but a number of wildfires are currently burning in the area, so Bud's rains may also do some good, by extinguishing these fires.
Jeff Masters
The views of the author are his/her own and do not necessarily represent the position of The Weather Company or its parent, IBM.
Cat 6 lead authors: WU cofounder Dr. Jeff Masters (right), who flew w/NOAA Hurricane Hunters 1986-1990, & WU meteorologist Bob Henson, @bhensonweather


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"Women are like labradors...,they all have their quarks."~Phil Robertson
And I really never follow what Ted would say.
FC Tribute to Justice, JH "Honor"
FC AFC Contempt of Court "Ruckus"
Medal Of Honor, QAA "Valor"
HRCH Kirby's High Sierra, SH, QAA "Kirby" Feb. 19, 2002 - Aug. 14, 2014
HRCH Niki Snowbird, SH, QAA "Niki" July 22, 2001 - May 11, 2015
Southland Order In the Court, QAA "Gavel" July 17, 2002- March 24, 2013
Southland Rusty Nail - derby points, qual placements "Rusty"
Disoderly Conduct "Chaos" -qual placements
I have learned I need these dogs much more than they need me. Tim Bockmon
It was the National Am. but no matter... What are the qualifications to judge these events.WTH he judged the National
From this outsider's perspective, Judging a National is as political as as it gets in the sport .
"i guess the old saying 'those of us that think we know everything annoy those of you that does' " --bobbyb 9/13/06
"A Good Dog is a Good Dog"
I watched Babe as well as later Daisy 100% of time select the long bird , passing the short bird rater in goose field or on river.
I seen Babe 100% time chase and select cripples over dead birds. In fact once she was chasing a cripple in a area with other ducks dropped. She came across a dead duck and started back with it. Spite it out is more like it and started mad search for the cripple . Which she got.
I seen Babe 100% of time with many dead geese dead on the ground search and look for cripple . And in fact , If she had a dead goose in mouth would spin and look at the flock flying off. If there was a cripple in the air, she would drop the bird and chase the flock , many times coming back with the cripple that dropped out of the air.
I call that :: Productive Reasoning :: The dog was born with it. Experience made her what she was, literally 100's of wild bird retrieves on the River and fields. !!
Some cripples are best not chased on the river. Let them go and call the dog back. A healthy cripple that is . Then get in the boat and drop way down below and let the dog run the bank back up to where last seen the duck as I would motor up river . Then it was possible to get this healthy cripple when the dog found it. I never seen a dog as good as Babe was at that. Hunting a flooded Island or river in high water is no play ground.
The only thing I miss about the river is The dogs that passed away.

subset: commoncrawl


text: The Allan Tannock Weir is situated on the Warrego River five kilometres south of Cunnamulla. There is a picnic area with wood fuel barbecue, swimming and fishing are permitted one hundred metres from the Weir Wall. A boat ramp is situated five hundred metres up river from the Weir. The area is shaded by River Red Gums, Coolibahs and Tea Trees. There are walking trails and prolific birdlife. Bird lists are available from the Cunnamulla Visitor Information Centre. The Allan Tannock Weir is part of the Stock Route and historically known as Keane's Crossing.


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Detoxify the skin from within. Ideal for teens and anyone who suffers from excessive oiliness and feels it makes their Acne condition worse. The products are created to treat and prevent Acne while not drying out the skin. Drying out the skin can often lead to a rebound effect (ie. More Acne forming than before treatment). Therefore these products use a more balancing approach through the use of alpha and beta hydroxy acids, mineral heavy clay, a water-based moisturizer, and gentle cleanser.
This detoxifying regimen of troubled skincare products helps minimize excessive greasiness and leaves the skin refreshed and supple. After 3 days of use, one should see an improvement not otherwise seen if skin were left untreated. Skin should be cleansed with the Gentle Cleansing Gel twice per day. After cleansing at night, the Botanical Acne Mask can be applied as directed. After rinsing the mask off, treat affected areas with the Derma Cleanse Acne Gel and moisturize with the Oil-Free Day Lotion. The mask can also be used overnight as a spot treatment to affected areas. The mask should be allowed to dry. Reduces the severity of the breakout overnight.


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Understand she had to come back. But was the bird in mouth? I ask, cause I had one that would go like hell to retrive. then sit there and look at the bird as if what do i do now. I would real him in without the bird in mouth. The usual progression is bumper, frozen bird, dead fresh bird, then live birds.
Ultimately the problem was fixed by ff. Good luck to you with dem nasty ol birds!
Ps i have some from last year. Just tossed a few for a friend. They worked


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Sorry Elaine, Faking It Blows
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Everyone gets to work their mouth. It's the American way. In sport, no place works the mouth like ESPN. On the whole, their people are likeable and their programming entertaining. But even The Worldwide Leader in Sports has its seamy side. And that would be the opinionators. The guys at ESPN who get paid to push the envelope. Speak first, (maybe) think later is their creed. On the NFL beat ...


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This FrontRunners analysis is a data-driven assessment identifying products in the Retail Management software market that offer the best capability and value for small businesses. For a given market, products are evaluated and given a score for the capability (x-axis) and value (y-axis) they bring to users. FrontRunners then plots the top 25-30 products in a quadrant format.
In the Retail Management FrontRunners infographic, the Capability axis starts at 3.1 and ends at 4.3, while the Value axis starts at 3.2 and ends at 4.6. Scales may differ between quadrants in order to capture the relative positioning of the specific products in each category.
To be considered for the Retail Management FrontRunners, a product needed a minimum capability user rating score of 2.5 and a minimum value user rating score of 2.5. All products that qualify as FrontRunners are top performing products in their market. The quadrant positions a product relative to its peers in the market. Each product falls within a designated quadrant based on their axis scores. Dependent on the specific needs of the software buyer, a product placed in any quadrant category could be a good fit. Each quadrant category has a distinct description for placement.
Upper Right = Leaders: Leaders are all-around strong products. They offer the highest value and capability in that market.
Upper Left = Masters: Masters may have fewer capabilities, but end users value those capabilities highly. Depending on the functionality needed, a product positioned in the Masters quadrant might be a better option to consider than products positioned in other quadrants.
Lower Right = Pacesetters: Pacesetters may offer a strong set of capabilities, but are not rated as high on value. For example, a Pacesetter might have a breadth of functionality at a higher price point.
Lower Left = Contenders: Contenders are strong-performing products that have not yet achieved the Value and Capability of the products in the other quadrants. For example, products in this quadrant may be more suited for companies that need more specialized functionality that comes at a price.
Download the full FrontRunners for Retail Management report.
The FrontRunners methodology assesses and calculates a score for products on two primary dimensions: Capability on the x-axis and Value on the y-axis.
The Capability score is an overall weighted average of scores including:
The Value score is an overall weighted average of scores including:
Markets are defined by a core set of functionality, and products considered for, and included in, FrontRunners must offer that core set of functionality. Additional related functionality can contribute to the capability score for a product. To qualify for consideration in FrontRunners for a software category, a product must have at least 10 unique user-submitted product reviews across the three Gartner Digital Markets web properties: softwareadvice.com, capterra.com and getapp.com.
The FrontRunners methodology assesses products on two primary dimensions: Capability on the x-axis and Value on the y-axis. Products receive a score between one and five for each axis. Products that meet a minimum score for each axis are included as FrontRunners. The minimum score cutoff to be included in the FrontRunners graphic varies by category, depending on the range of scores in each category. For products included, the Capability and Value scores determine their positions on the FrontRunners graphic.
The Capability score is based on three criteria: user ratings on capability, a functionality breadth analysis, and a business confidence assessment.
For each of these two data points, the methodology calculates the percentile ranking for each product relative to all other products in the software category that have qualified for FrontRunners consideration. That percentile ranking is then translated into a one to five score.
If the company's size and product's customer base are both significant and growing, then the likelihood that the business will invest in the product is higher than in the alternative scenarios. For each of these four data points, the methodology calculates the percentile ranking for each product relative to all other products in the software category that have qualified for FrontRunners consideration. That percentile ranking is then translated to a one to five score.
The overall one to five Capability score is a weighted average of the scores for user ratings, functionality breadth and business confidence.
The Value score is based on two criteria: user ratings on value and product adoption.
For each of these four data points, the methodology calculates the percentile ranking for each product relative to all other products in the software category that have qualified for FrontRunners consideration. That percentile ranking is then translated into a one to five score.
The overall one to five Value score is a weighted average of the scores for value user ratings and product adoption.
Data sources include user reviews and ratings, public data sources and data from technology vendors. The user-generated product reviews data incorporated into FrontRunners is collected from submissions to all three Gartner Digital Markets sites (softwareadvice.com, capterra.com and getapp.com). As a quality check, we ensure the reviewer is valid, that the review meets quality standards and that it is not a duplicate.
The business confidence and product adoption data comes from public sources, collected by either a third-party data provider or by Gartner associates. As a quality check, we compare this data against data submitted by the providers. We use this data to calculate a product's percentile ranking, which allows us to determine how products compare relative to one another rather than determine an absolute number.
The functionality breadth data is collected from the technology providers. We check the data provided and challenge data that seems inflated or unlikely. We use this data to calculate a product's percentile ranking, which allows us to determine how products compare relative to one another rather than determine an absolute number.
See FrontRunners frequently asked questions (FAQ) for more information on the methodology.
Providers must abide by the FrontRunners External Usage Guidelines when referencing FrontRunners content. Except in digital media with character limitations, the following disclaimer MUST appear with any/all FrontRunners reference(s) and graphic use:
FrontRunners scores and graphics are derived from individual end-user reviews based on their own experiences, vendor-supplied information and publicly available product information; they do not represent the views of Gartner or its affiliates.
Providers listed as Runners Up were eligible for inclusion in the FrontRunners quadrant, including having 10+ product reviews, but their value or capability axis score was not high enough for positioning on the FrontRunners quadrant.
Retail Point of Sale (POS) systems, also known as POS software, have come a long way from being bolt-on applications for cash registers. Today, the cash register as the cornerstone piece of retail technology has been replaced by PCs, tablets and mobile devices.
Retail software vendors offer integrated software programs and POS systems for "mom-and-pop" stores to large retail chains, and everything in between. Retail software applications handle any combination of checkout, inventory control, customer management, e-commerce sales, merchandising and distribution. These systems help retailers automate the point of sale, improve inventory tracking and enable more effective management of customer data to grow profits and decrease store inefficiencies.
Continuously falling hardware and equipment costs, the emergence of mobile devices like iPads and new cloud-based POS offerings have led to more choices than ever. This leaves buyers with a daunting challenge as they try to determine the best application for their needs. The goal of this buyer's guide is to help retailers understand the market as they begin their research. What we'll cover:
Common Features of Retail Software
Specialty Retail Software Solutions
Benefits of Adopting Retail Software
Report: Buyers' Top Reasons for Evaluating Retail Software
How Is It Priced?
Tips for New Buyers
Market Trends to Understand
Recent Events You Should Know About
For buyers that manage a single store, the most important features to look for include:
Retail software products are generally straightforward, helping retailers ring up customers, update inventory levels, present basic reports and keep track of customers.
|Point of sale (POS)
|Helps sales clerks ring up customers and process payments. Ensures cashiers charge the correct amount, adjusts inventory and prints receipts.
|Inventory control
|Automates the management of supply levels. Deducts inventory as sales are completed and provides alerts when inventory levels reach pre-defined thresholds. Also provides reports on inventory movement trends.
|Retail accounting
|Centralizes accounting data and provides accurate details on business performance. Incorporates inventory figures as well as other expenses, such as payroll and rent.
|Retail CRM
|Stores customer information and purchase history. Enables retailers to track contact information, key dates such as birthdays and anniversaries and preferred items to market to customers.
In general, we recommend single store owners select solutions based on budget, business size and IT capabilities.
When it comes to managing a retail business, the most difficult jump for retailers comes when they transition from one storefront to two. This is also the case for technology purchases, and complexities continue to build as the number of storefronts increase. And while this traditionally meant adding new locations and real estate, additional storefronts today can be both physical and on the Web.
These retailers commonly need applications with advanced features or an enterprise application suite to help manage their business. As a simple rule, you should consider these options if you:
Retail buyers evaluating more advanced applications generally have two options:
Retail software suites. Buyers evaluating these solutions are generally looking for one application suite to manage the entire retail operation. These systems are typically scalable with robust multi-location reporting, centralized pricing controls and potentially warehouse or transportation management. Ideal for retailers with either a large number of stores or very large stores.
Best-of-breed retail applications. Buyers evaluating these solutions are generally looking for a stand alone application to manage one function within the retail operation, such as accounting, merchandising or warehouse management. They typically have made large investments in existing systems and are seeking best-of-breed solutions to complement them.
In addition to the core modules listed in the chart above, these application suites typically include merchandising, warehouse and transportation management and business intelligence functionality. The breadth and complexity of the technology you select should depend on your business' size, number of storefronts and number of stock-keeping units (SKUs). We've summarized the applications you will find in an enterprise retail software suite below.
|Merchandise management
|Enables buyers to create the optimal balance of SKUs. Provides analytical tools to plan merchandise based on sales histories, trends and forecasts.
|Warehouse management
|Automates inventory control within the warehouse. Functions include picking, packing, pulling and labor management.
|Transportation management
|Helps organizations efficiently transport inventory from distribution centers to store locations and customers. Enables enterprises to plan shipments via air, land or sea with their own or via third-party fleets.
|Business intelligence
|Allows retailers to make better decisions using both internal and external data. Larger retailers will often use BI tools to improve merchandising and marketing efforts. Retailers may invest in BI modules within existing enterprise suites or purchase stand alone BI tools.
Retailers might want to consider software designed specifically for the unique needs of their business. For example, restaurant and food service business owners often require restaurant software to process orders, print tickets, analyze ingredient availability and determine how much to charge for meals. Or, jewelers might need jewelry POS software to manage repairs and quotes, in addition to processing sales and inventory tracking.
Here are some other examples:
Software for resale stores. Unlike other retailers, consignment, pawn shop and resale store owners don't own their inventories. In fact, the providers may later want their inventory back. These retailers need retail software solutions with inventory management and accounting functionality tailored to these store types.
Software for cellular phone stores. These retailers need software with advanced CRM capabilities to know which phones and accessories customers have already purchased, and where they're at within their contract periods. This information is greatly beneficial when it comes to upsells. Many of these systems also include domain-specific features, such as the ability to manage cellular data plans, phone activations and commissions tracking for employees.
Software for grocery stores. For grocers, speed and accuracy are necessary at the point of sale to help move customers through the line quickly while maintaining accurate inventory counts. Integration with scales, barcode scanners and other hardware peripherals are crucial features in these systems. In addition, grocers should look for solutions that support their delicatessen, bakery and butcher departments.
Outside of POS, there are other types of software that serve specialty retailers. Companies that sell tickets - like theaters and sporting facilities, for example - might opt for systems that specialize in that functionality. In such cases, buyers should ensure the POS they're considering also integrates with their existing or future ticketing system.
A properly implemented system should help retailers increase sales, increase inventory turns, minimize unsold inventory and manage the company more efficiently. The primary benefits that can be realized by implementing new retail management software include:
More efficient transactions at the point of sale. One of the most important functions of retail software is to improve the checkout process for both employees and customers. POS applications integrate with cash drawers, external displays, printers, barcode scanners, scales and credit card terminals to reduce customer wait times and create a log of both inventory movement and individual customer purchases.
Outdoor and sporting goods store Orvis selected the Epicor retail software solution to upgrade its outdated point of sale technology. With Epicor, Orvis was able to achieve a tenfold increase in processing speeds at the point of sale and a 30-second drop in average credit card transaction processing times. The software also helped Orvis build-out its database with customer ZIP codes and email addresses for future marketing opportunities.
Improved inventory control and tracking. The goal for any retailer is to maintain proper inventory levels and never to run out of popular items. This is difficult when retailers aren't sure how particular SKUs are performing. Inventory management functionality gives retailers this insight and helps them make sound inventory decisions.
After the Museum of New Mexico Foundation Shops (MNMFShops) implemented the WinRetail solution, MNMFShops was able to identify its most popular and slowest-moving items. MNMFShops re-prioritized its inventory around this analysis, and was able to reduce its bloated inventory of books by $25,000 in the process.
Centralized customer management. Customer relationship management (CRM) modules help retailers better serve customers through personalized interactions. These modules utilize databases that allow retailers to serve targeted email offers and regular promotions to customers, while measuring the impact of these programs. Additionally, contact management features help retailers provide a more personalized experience for both online and offline shoppers.
Guitar Center Pro invested in the NetSuite Retail CRM module to help improve its quoting process and better prioritize the assignments of its sales team. After replacing its existing applications and Excel spreadsheets, Guitar Center Pro was able to reduce its average time spent quoting from five hours to one hour per week, while achieving 12 percent annual growth in its stores.
Greater ability to cut costs. Retail technology reduces the time spent manually entering data, freeing retailers to spend more time analyzing employee, inventory and business performance. Many solutions include custom report wizards, employee commission tracking and dashboards to quickly identify top sales performers and areas for business improvement.
South Korean supermarket Lotte Mart deployed JDA Software in a phased approach to improve its pricing strategy and planning at the store level. Improved insight into how individual outlets should markdown, order and display items is one reason Lotte Mart saw a 12 percent increase in sales and a 25 percent decrease in stock levels.
Over the years, we've spoken with thousands of retailers considering new point of sale software solutions, providing us with unique insight into buyers' common pain points and motivations for purchasing new systems. In this report, we analyzed a sample of 385 random interactions with retail buyers to discover their top reasons for buying.
We found that the main reasons retailers are replacing their existing POS methods is to improve efficiency, modernize their systems and gain new POS functionality. Read the entire report for the full results, which you may find helpful in informing your software purchasing process.
Cloud-based retail POS software is typically priced on a per-terminal, per-month basis, with some vendors offering discounts if you pay annually instead of monthly.
On-premise software, on the other hand, is usually priced by the number of perpetual licenses required for each terminal, with fees typically paid upfront for the right to use the software in perpetuity (rather than paying a monthly or annual subscription).
Regardless of whether the software uses a perpetual license or subscription pricing model, vendors usually offer packages with varying levels of functionality based on the breadth and depth of features required by retailers.
Reviewing new retail point of sale software can be intimidating because of the many available choices (here are some of the most popular solutions). We recently surveyed software buyers from a variety of industries to determine which tactics work best when reviewing different systems. Their most recommended methods include evaluating vendor references (i.e., feedback from real customers) and having an attorney review the agreement before signing.
Quadrant indicating where selection tactics fall on the "impact" and "satisfaction" spectrum
Following selection methods in the "most effective" quadrant and avoiding those in the "least effective" quadrant (e.g., involving end users in the selection process) can help you make a better decision and avoid wasting valuable time.
We commonly hear from buyers that are evaluating POS solutions for the first time and looking at POS reviews for the first time. Questions we commonly hear include:
From our perspective, it's hard to label one solution as the best POS software solution for every retailer. We've reviewed the top POS systems for retail and found that regardless of system or buyer, there are a number of steps that can help make your point of sale software review process smoother:
Research the market first. Vendor websites are a good place to start your research and read up on retail point of sale system reviews. Understand that vendors often use phrases like "cashier software" and "cash register software" to describe their solutions, but these terms are synonymous with point of purchase software.
Prioritize your needs. While many solutions can meet your basic needs, you may need specific functionality in the new system. Do you need integrated e-commerce functionality? Is it vital that the vendor have experience supporting retail software for small business? Would you prefer to invest in open source POS software? Keep these priorities top-of-mind while reading through various POS system reviews.
Traditional vendors embrace the iPad. A shortlist should be compiled that lists the best retail point of sales systems that meet your priorities. Narrowing down the best POS systems can effectively shorten the system search and ensure that you only evaluate systems that will be a good fit. That's where we come in—we're here to help put together the right shortlist.
Evaluate solutions based on demos. POS software reviews are a good place to start when evaluating systems, but the final step should be participating in solution demos. Here, you can test-drive the solution and find the best retail POS system for you.
As you evaluate a new point of sales system, keep these trends in mind. How your vendor fits within these trends could have a big impact on their viability.
Mobile and digital currency. Payment options such as PayPal, Google Wallet and Bitcoin will become mainstream, allowing consumers to use digital currencies to pay for items.
Mac vs. PC. A growing number of retailers are shifting from proprietary hardware solutions and personal computers to Apple products, like Mac computers and iPads. These retailers will need to ensure that the software they select—and the specific features they want, which are sometimes not available across platforms—run on Mac, iPad- or iPod-devices.
Mobile POS. As more and more retailers conduct sales at tradeshows, events and other temporary locations, mobile POS applications are becoming increasingly common. These systems enable users to process payments wirelessly and access inventory/sales data remotely. With the popularity of Apple's iPad, more vendors are developing iOS-optimized versions of their traditional applications.
Change is an iPad cash register app and mobile POS software
CRM technologies. Predictive modeling can be used to recommend items to cross-sell and upsell for new revenue-generation opportunities. Social media data will also be integrated so influential users can receive perks that encourage them to publicize a business by checking in online or uploading photos.
Order-ahead functionality. With many consumers no longer waiting in line to buy, the ordering experience will become more streamlined and intuitive.
POS gamification. POS systems will use popular technology such as Yelp and Foursquare to offer gamification incentives that provide benefits for both retailers and customers.
"Intelligent" inventory management. More advanced applications, such as merchandise management and open-to-buy, are enabling users to make more intelligent, data-driven purchasing and inventory decisions.
Lightspeed POS launched an e-commerce solution. The new offering is called Lightspeed eCom and integrates brick-and-mortar retail with an e-commerce presence and syncs the disparate inventories as well. Lightspeed eCom has been integrated with Lightspeed Retail, its cloud-based POS solution. It also integrates and synchronizes online and retail store inventory, sales figures and customer sales data while enabling the retailer to shift stock quickly between channels.
Samsung and payment processing provider Total Merchant Services released the Groovv POS Flex. Groovv is designed for SMBs and features a Samsung Galaxy Tab and an EMV-compliant, NFC-enabled payment processing device that is pre-programmed with software for inventory management, reporting and integrated marketing. The technology brings Samsung into the mobile POS space, as store associates can detach the tablet to roam a store with the consumer. The system connects wirelessly to peripherals, including a cash drawer receipt printer, barcode scanner and kitchen printer, so that retailers can customize their setup to match their environment and needs.
Fujitsu launched an innovative software solution for wearable devices. It creates a two-way, secure and collaborative digital communication platform between Fujitsu U-Scan Self-Checkout (SCO) or Fujitsu Fresco Point-of-Sale (POS) touch-screen systems and Samsung wearable devices. The software allows employees to handle their core duties, while also having hands-free access to important alerts and messages that ensure the entire store is operating smoothly. It promotes increased staff responsiveness and overall store efficiency in grocery, convenience and retail environments.
Our service is simple and 100% free to customers like you because software vendors pay us when we connect them with quality leads. You save time and get great advice. Vendors get great referrals. It's a win for everyone!


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UFC welterweight fighter Mike Pyle prepares for UFC 160 at the Syndicate gym Monday, May 20, 2013. Pyle will fight Rick Story at the MGM Grand Garden Arena Saturday.
Mike Pyle stays humble, hungry ahead of UFC 160 by remembering his roots
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Contact: Lauren Robinson-Brown (609) 258-3601


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Balticon 2009 in Strobe Flashes
I'm really bad at doing thorough con wrap-ups, as evidenced by the fact that I usually don't actually finish them. I though about presenting my Balticon 2009 wrapup as a compressed novel in honor of the recently late but always great JG Ballard but that turned out to be really difficult. Imagine that. That is […]Tags: balticon, chris lester, davidghartwell, davidmoldawer, earlnewton, erkpod, evoterra, geistbear, hugh macleod, jimvanverth, johncmar, kathryncramer, keithradecandido, mattwallace, mur lafferty, paulfischer, phil rossi, rosscott, thomas gideon, tom vincent


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New This Week: School of Seven Bells, Trust & More
By J. Edward Keyes, Editor-in-Chief
Man. There are just so many new records today. Also, I think about halfway through this, I developed carpal tunnel syndrome. Trust, TRST: Behind the year's worst album cover is one of the year's best records. Super goth, in all the right ways. Where my Apoptygma Berzerk fans at? Home crying? Cool. See you there. This one is HIGHLY RECOMMENDED Barry Walters goes: Trust is danceable even if you're not stuck in a K-hole. Its tempos vary… more »


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Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads
DOI: 10.1186/gb-2011-12-2-r13
© Turro et al.; licensee BioMed Central Ltd. 2011
Received: 19 September 2010
Accepted: 10 February 2011
Published: 10 February 2011
We present a novel pipeline and methodology for simultaneously estimating isoform expression and allelic imbalance in diploid organisms using RNA-seq data. We achieve this by modeling the expression of haplotype-specific isoforms. If unknown, the two parental isoform sequences can be individually reconstructed. A new statistical method, MMSEQ, deconvolves the mapping of reads to multiple transcripts (isoforms or haplotype-specific isoforms). Our software can take into account non-uniform read generation and works with paired-end reads.
High-throughput sequencing of RNA, known as RNA-seq, is a promising new approach to transcriptome profiling. RNA-seq has a greater dynamic range than microarrays, which suffer from non-specific hybridization and saturation biases. Transcriptional subsequences spanning multiple exons can be directly observed, allowing more precise estimation of the expression levels of splice variants. Moreover, unlike traditional expression arrays, RNA-seq produces sequence information that can be used for genotyping and phasing of haplotypes, thus permitting inferences to be made about the expression of each of the two parental haplotypes of a transcript in a diploid organism.
The first step in RNA-seq experiments is the preparation of cDNA libraries, whereby RNA is isolated, fragmented and synthesized to cDNA. Sequencing of one or both ends of the fragments then takes place to produce millions of short reads and an associated base call uncertainty measure for each position in each read. The reads are then aligned, usually allowing for sequencing errors and polymorphisms, to a set of reference chromosomes or transcripts. The alignments of the reads are the fundamental data used to study biological phenomena such as isoform expression levels and allelic imbalance. Methods have recently been developed to estimate these two quantities separately but no approaches exist to make inferences about them simultaneously to estimate expression at the haplotype and isoform ('haplo-isoform') level. In diploid organisms, this level of analysis can contribute to our understanding of cis vs. trans regulation [1] and epigenetic effects such as genomic imprinting [2]. We first set out the problems of isoform level expression, allelic mapping biases and allelic imbalance, and then propose a pipeline and statistical model to deal with them.
Isoform level expression
Multi-mapping reads. Approximate proportion of reads mapping to multiple Ensembl transcripts or genes in human using 37 bp single-end or paired-end data obtained from HapMap individuals.
37 bp single-end
37 bp paired-end
Multiple transcripts
Multiple genes
where X it are the (unobserved) counts of reads from region i of transcript t, b is a normalization constant used when comparing experiments, μ t is a parameter representing the expression of transcript t and s i is the effective length of region i (that is the number of possible start positions for reads in the region). This model can be fit using an expectation maximization (EM) algorithm, since the X it are unobserved but their sums across transcripts are observed.
This model has been used by [4] in their POEM software, with i representing exons. Their method does not use reads that span multiple exons or reads that map to multiple genes. The same model has been used in [5], with i representing exons or part exons, or regions spanning exon junctions, enabling good estimation of isoform expression within genes. They do not, however, include reads mapping to multiple genes. The RSEM method [6] employs a similar model, but models the probability of each read individually, rather than read counts. This method allows reads to come from multiple genes as well as multiple isoforms of the same gene. The modeling of individual reads allows RSEM to accommodate general position-specific biases in the generation of reads. However, two recent papers [7, 8] have shown that deviations from uniformity in the generation of reads are in great part sequence rather than position-dependent for a given experimental protocol and sequencing platform. Furthermore, the computational requirements of modeling individual reads increasing proportionately with read depth, which, in the case of RSEM, is exacerbated further by the use of computationally intensive bootstrapping procedures to estimate standard errors. None of the above methods are compatible with paired-end data. A recently published method, Cufflinks [9], focuses on transcript assembly as well as expression estimation using an extension of the [5] model that is compatible with paired-end data. However, this method does not model sequence-specific uniformity biases and uses a fixed down-weighting scheme to account for reads mapping to more than one transcription locus, meaning that the abundances of transcripts in different regions are estimated independently.
Allelic imbalance
Studies of imbalances between the expression of two parental haplotypes have mostly been restricted to testing the null hypothesis of equal expression between two alleles at a single heterozygous base, typically with a binomial test [1, 2, 10]. However, as transcripts may contain multiple heterozygotes, a more powerful approach is to assess the presence of a consistent imbalance across all the heterozygotes in a gene together. This has been done on a case-by-case basis using read pairs that overlap two heterozygous SNPs [11] while [12] propose an extension to the binomial test for detecting allelic imbalance that takes into account all SNPs and their positions in a gene. However, this approach, which is a statistical test rather than a method of quantifying haplotype-specific expression, assumes imbalances to be homogeneous along genes and thus does not take into account the possibility of asymmetric imbalances between isoforms of the same gene.
Allelic mapping biases
Aligners usually have a maximum tolerance threshold for mismatches between reads and the reference. Reads containing non-reference alleles are less likely to align than reads matching the reference exactly, so genes with a high frequency of non-reference alleles may be underestimated. Ideally, aligners would accept ambiguity codes for alleles that segregate in the species (cf. Novoalign [13]), but no free software is currently able to do this. A possible workaround is to change the nucleotide at each SNP to an allele that does not segregate in the species, as has been proposed to remove biases when estimating allelic imbalance [10]. However, in the context of gene expression analysis, this leads to even greater underestimation of genes with many non-reference alleles and an increase in incorrect alignments to homologous regions. Instead, we propose aligning to a sample-specific transcriptome reference, constructed from (potentially phased) genotype calls.
In this paper we present a new pipeline, including a novel statistical method called MMSEQ, for estimating haplotype, isoform and gene specific expression. The MMSEQ software is straightforward to use, fully documented and freely available online [14] and as part of ArrayExpressHTS [15]. Our pipeline exploits all reads that can be mapped to at least one annotated transcript sequence and reduces the number of alignments missed due to the presence of non-reference alleles. It is compatible with paired-end data and makes use of inferred insert size information to choose the best alignments. Our method permits estimating the expression of the two versions of each heterozygote-containing isoform ('haplo-isoform') individually and thus it can detect asymmetric imbalances between isoforms of the same gene. Our software further takes into account sequence-specific deviations from uniform sampling of reads using the model described in [8] but can flexibly accommodate other models. We validate our method at the isoform level with a simulation study, comparing our results to RSEM's, and applying it to a published Illumina dataset consisting of lymphoblastoid cell lines from 61 HapMap individuals [16]. We validate our method at the haplo-isoform level by showing we can deconvolve the expression estimates of haplo-isoforms on the non-pseudoautosomal (non-PAR) region of the X chromosome using a pooled dataset of two HapMap males. We further apply our method to a published dataset of F1 initial and reciprocal crosses of CAST/EiJ (CAST) and C57BL/6J (C57) inbred mice [2] and demonstrate that MMSEQ is able to detect parental imbalance between the two haplotypes of each isoform.
Overview of the pipeline
- (a)
Expression estimation using alignments to a pre-defined transcriptome reference,
- (b)
Expression estimation using alignments to a transcriptome reference that is obtained from the RNA-seq data.
In case (a), the level of estimation (haplo-isoform or isoform) depends on whether the reference includes two copies of heterozygous transcripts. In case (b), it depends on whether the genotypes are phased. The most exhaustive use of the pipeline proceeds as follows. First, the reads are aligned to the standard genome reference using TopHat [17]. Then, genotypes are called with SAMtools pileup [18]. Genotypes are then phased with polyHap [19] using population genotype data to produce a pair of haplotypes for all gene regions on the genome. The standard transcriptome reference is then edited for each individual to match the inferred haplotypes. The reads are realigned to the individualized haplotype specific transcriptome reference with Bowtie [20], finding alignments for reads that originally failed to align due to having too many mismatches with the standard reference (approximately 0:3% more reads recovered, with some transcripts receiving up to 13% more hits, in the HapMap dataset [16]). Finally, our new method, MMSEQ, is used to disaggregate the expression level of each haplo-isoform.
Poisson model
We use the model in Equation 1 as a starting point for modeling gene isoforms and extend it to apply to haplo-isoforms. First, we employ a more general definition of 'region': each read maps to one set of transcripts, which may belong to the same gene or to various different genes, and which can have two versions, one containing the paternal and the other the maternal haplotype. These sets are labeled by i. Many reads will map to the exact same set, hence we can model reads counts (k i ) for the set. The M it are defined very straightforwardly as the indicator functions for transcript t belonging to set i. The region length s i is the effective length of the sequence shared between the whole set. If the set of transcripts all belong to the same gene and haplotype, then s i may be the effective length of an exon or part exon. However, aligned reads often map to multiple genes equally well (Table 1) so the region need not correspond to an actual region on the genome. Using our definition of a region, the s i would be difficult to calculate given the sheer number of overlaps and regions, but in fact the s i are not needed in the calculation of the model (see Materials and Methods). Hence we have a model for read counts in which the data and fixed quantities (k i and M it ) are calculated in a straightforward way, and which allows for reads mapping to multiple isoforms of the same or different genes in exons or exon junctions and to paternal and maternal haplotypes separately.
where is an adjusted effective length, referred to as the sum of sequence preferences (SSP) in [8]. We use their Poisson regression model to adjust the length of each transcript based on its sequence, but other adjustment procedures may be used instead. Briefly, the logarithm of the sequencing preference of each possible start position in a transcript is calculated as the sum of an intercept term plus a set of coefficients determined by the sequence immediately upstream and downstream of the start position. It would also be possible to integrate the method described in [7], which uses a weighting for reads based on the first seven nucleotides of their sequences, by applying this weighting in our calculation of k i . However, this approach does not incorporate the effects of the sequence composition on the reference upstream of the read start positions or further downstream than seven bases, and we thus prefer to use the [8] method instead. The normalization constant b is used to make lanes with different read depths comparable. We set b to the total number of reads (in millions) and measure transcript lengths in kilobases, which means the scale of the expression parameter μ t is equivalent to RPKM (reads per kilobase per million mapped reads) described in [3]. In downstream analysis, a more robust measure can be used, such as the library size parameter suggested by [21].
The only unknown parameters in the model are the μ t . The observed data are the k i and the matrix M and effective transcript lengths l t are known. In principle the effective lengths of the transcript sets s i can be calculated, but in fact, they are not needed (see Materials and Methods).
The maximum likelihood (ML) estimate of μ t cannot be obtained analytically, so instead we use an expectation maximization (EM) algorithm to compute it, an approach also taken by [4, 6] for isoforms. After convergence of the algorithm, we output the estimates of μ t and refer to them as MMSEQ EM estimates.
Again, the only lengths needed are the l t . The conjugacy of the Poisson-Gamma model makes the sampling fast and straightforward as the full conditionals are in closed form (see Materials and Methods). We use the final EM estimate of the μ t as the initial values for the Gibbs sampling. We then produce samples from the whole posterior distributions of the μ t and calculate the sample means and their respective Monte Carlo standard errors (MCSE), which take into account the autocorrelations of the samples [22]. We set the hyperprior parameters to α = 1.2 and β = 0.001, producing a vague prior on the μ t that captures the well-known broad and skewed distribution of gene expression values. We output the means of the Gibbs samples of μ t , which we refer to as MMSEQ GS estimates. As we shall show, the regularization afforded by the Bayesian algorithm produces estimates with a lower error than the MMSEQ EM estimates. Moreover, it can readily be shown that for transcript with low coverage, the ML estimate is often zero, even though this is likely to be an underestimate of the expression. For example, suppose there exist two equally-expressed haplo-isoforms differing by only one heterozygote. Under the assumption of uniform sampling of 0.01 reads per nucleotide for both haplo-isoforms, if the read length is 35, then the probability of observing a read containing one allele but no reads containing the other allele is fairly high (2(1-e-0.35)e-0.35 ≃ 0.42). The ML estimate of the haplo-isoform with the unsampled allele under this scenario is zero while the ML estimate of the haplo-isoform with the sampled allele is overestimated. With Gibbs sampling, on the other hand, this effect is tempered by the Gamma prior. The MMSEQ GS estimates are thus our preferred expression measures.
Best mismatch stratum filter
While a read may align to multiple transcripts, not all alignments may be equally reliable. We therefore filter out all alignments that do not have the minimal number of mismatches for a given read or read pair (similar to the --strata switch in Bowtie, but compatible with paired as well as single end data). In the case of paired-end data, the number of mismatches from both ends is added up to determine the 'mismatch stratum' of a read pair. This filter is crucial in order to correctly discriminate between the two versions of an isoform at a heterozygous position, since reads from one haplotype also match the alternative haplotype with an additional mismatch. The stratum filter thus ensures that reads are properly assigned to the correct haplotype.
Insert size filter for paired-end data
For paired-end data, both reads in a pair must align to a transcript for the mapping to be considered. If the fragments are sufficiently large, the alignments may span three exons and align to transcripts that both retain and skip the middle exon. However, the alignment with an inferred fragment size (also called insert size) that is nearer to the expected insert size from the fragmentation protocol, is more likely to be correct. We exploit this information by applying an insert size filter to alignments in the best mismatch stratum for each read. If an alignment's insert size is nearer than x bp (for example equivalent to one standard deviation) away from the expected insert size, then all other alignments for that read with an insert size greater than x bp away from the expected insert size are removed. This filter can be thought of as an extension of mismatch-based filtering for reporting only alignments with moderately high probability of being true. Although full probabilistic modeling is more principled, filtering is a commonplace approach to reducing alignment candidates for each read to a set that can be dealt with pragmatically. For the HapMap dataset, mistakes in the protocol resulted in two distributions of insert sizes within some samples, so we omitted this filter.
MMSEQ output
The mmseq program produces three files each containing EM and GS expression estimates with associated MCSEs. The first file provides estimates at the transcript/haplo-isoform level, the second file provides aggregate estimates for sets of transcripts that have been amalgamated due to having identical sequences (and therefore indistinguishable expression levels), and the third file aggregates transcript estimates into genes, thus providing gene-level estimates. Homozygous transcripts are aggregated together, whereas heterozygous transcripts are aggregated separately to produce 'haplo-gene' level estimates. With respect to transcripts that have identical sequences and hence indistinguishable and unidentifiable expression levels, the posterior samples exhibit high variance and strong anti-correlation but the sum of their expression can be precisely estimated (Additional file 1). We therefore recommend use of the amalgamated estimates.
Performance and scalability
mmseq performance. Performance of the mmseqprogram on subsets of different sizes of the HapMap paired-end dataset.
Read pairs (millions)
Dimension of M
Runtime (seconds)
63,924 × 68,666
84,417 × 75,649
97,576 × 79,035
107,344 × 81,289
134,489 × 86,528
166,100 × 91,023
Correction for non-uniform read sampling
Simulation study of isoform expression estimation
Comparison of isoform expression estimation between MMSEQ and RSEM
Like MMSEQ, the RSEM method [6] makes use of all classes of reads to estimate isoform expression. The authors have shown an improvement of their method for gene-level estimation over strategies that discard multiply aligned reads or allocate them to mapped transcripts according to the coverage by single-mapping reads (as in [3]). However, isoform-level results for their method have not been assessed. We obtained RSEM estimates for Ensembl transcripts using our simulated human sequence dataset for the purposes of comparison.
We scaled our simulated and estimated expression values to add up to one in order to make them comparable to RSEM's fractional expression estimates. We found that RSEM and MMSEQ EM are comparable but, unlike the MMSEQ EM algorithm, RSEM tended to overestimate some medium-expression transcripts. Both the RSEM and MMSEQ EM algorithms tended to underestimate some low-expression transcripts, pushing them very close to zero and thus producing very large errors on the log scale. This was avoided by the regularization of the Gibbs algorithm, which produced tighter estimates and only overestimated slightly some very lowly expressed transcripts (Figure 5 and Additional file 5), showing the benefits of using the whole posterior distribution of μ t to estimate expression rather than a maximization strategy.
Isoform-level application to the HapMap dataset
Although the ordering of transcripts and genes was broadly maintained even between lanes belonging to different individuals and runs, we found a striking contrast in the distribution of expression values between lanes of the same individual and lanes of different individuals (Additional file 6). The consistency of expression values for lanes of the same individual indicates that the technical replicability of the Illumina GAII sequencer is extremely high and therefore that the variation observed between lanes from different individuals is mostly a reflection of biological variability. This is in line with previous research showing that sequence count data follow a negative binomial distribution in biological replicates and a Poisson distribution in technical replicates [21]. As such, we expect the variance of our estimates to be proportional and greater than proportional to the expression values for technical and biological replicates respectively. This is indeed borne out both at the gene and transcript level (Additional file 7) and corroborates the need to take into account extra variability for highly-expressed transcripts in differential expression analysis with biological replication (see Discussion).
Validation of haplo-isoform deconvolution
The non-pseudoautosomal region (non-PAR) of the X chromosome in human males is haploid, and thus the alleles in that region can be called directly without the need for phasing. We validated our method for deconvolving expression between two haplotypes of the same isoform as follows. We used the RNA-seq data of two males from the HapMap data (NA12045 and NA12872) to call their haplotypes. We identified 117 isoforms on the non-PAR of the X chromosome that differed between the two individuals. We created custom transcriptome references for each of the two males, containing their individual versions of the 117 isoforms. We then created a third hybrid reference containing two copies of the 117 isoforms, one matching the haplotype of one male and the second matching the haplotype of the other. This hybrid reference mimics the case of a female with two X chromosomes with unknown expression of the two parental copies of each isoform. We obtained individual expression estimates of the 117 isoforms using the separate transcriptome references in each male and compared them with estimates obtained by aligning a dataset pooled from the data of both males to the hybrid reference. Although the original correlation between the two males was 0.85, the correlation between the individual estimates and the deconvolved estimates was 0.96 and 0.98, showing MMSEQ is capable of disaggregating the expression from paternal and maternal isoforms (Additional file 8).
Demonstration of haplo-isoform expression estimation using an F1hybrid mouse brain dataset
We have applied MMSEQ to a published murine embryonic day 15 RNA-seq dataset of CAST/C57 initial (F1i) and reciprocal (F1r) crosses [2]. Each RNA sample was a pool from four individuals. The C57 reference transcriptome used by the authors is available from the UCSC Genome Browser [23]. The authors called SNPs by aligning reads from the CAST samples to the C57 reference. We created a CAST reference transcriptome by changing alleles in the C57 reference sequences according to those SNP calls. The two references were combined in a hybrid reference containing two entries for isoforms that differed in sequence between C57 and CAST. Thus there is a one-to-one mapping between SNPs called in the parents and heterozygotes in the hybrids. The data consist of 152 and 159 million 36 bp Illumina GAII reads for F1i and F1r respectively.
We also identified a clustering of transcripts that exhibited CAST overexpression in the F1i hybrids but approximately balanced expression in the F1r's. We identified the cluster as consisting wholly of transcripts on the X chromosome (Additional file 9), which suggests that the initial crosses were male and the reciprocal crosses female. The sexes of the hybrid mice are in fact unknown. There was a slight skew in favor of the CAST strand in the reciprocal crosses. We think it is unlikely that this was due to mapping biases, since the CAST reference was produced from SNP calls against the C57 reference and was thus of lower quality, so any mapping bias would be expected to be in favor of C57. Moreover, [24] found a similar skew in adult samples of the same crosses. It is possible that the skew is the result of a selective bias in favor of C57 X-inactivated cells [25], possibly caused by one or more of the three mutations on the X-inactivation transcript (UCSC ID uc009tzp.1) or mutations in its promoter region.
The third grouping in the plot is on the lower-left to upper-right diagonal. These transcripts demonstrate consistent CAST/C57 differential expression regardless of the sex-strain combination of the parents, and are thus indicative of cis regulation.
One advantage of MMSEQ is that imbalances are assessed at the transcript level rather than for individual SNPs. Thus it is not necessary to set arbitrary thresholds on the numbers of heterozygotes or the magnitude and significance of the imbalances to make claims about transcript-level imbalances. Indeed, some of the transcripts that contain one or more heterozygote with a significant P-value but were not classified as 'consensus imprinted' by [2] are clearly shown to be imprinted by our results. Note however that 27 transcripts had significant heterozygotes with imbalances in opposing directions, demonstrating that it is not always appropriate to generalize from a single locus to make claims of imbalance at the transcript level (Figure 8 and Additional file 10).
MMSEQ estimates for H13 and Mcts2 isoforms in F1 hybrid samples. MMSEQ estimates for each haplotype and isoform of H13 and Mcts2of the initial and reciprocal crosses are shown.
CAST i
C57 r
C57 i
CAST r
We have presented a pipeline and statistical method that can disaggregate expression between isoforms and even between the two haplotypes of each isoform within an individual. MMSEQ produces improved isoform estimates compared to RSEM for medium to low expression transcripts, is more scalable, and estimates standard errors more efficiently. Furthermore, our principled approach to haplo-isoform quantification obviates the need for ad-hoc interpretations of SNP-by-SNP imbalances in terms of transcripts. Two aspects of our method, however, deserve further discussion.
Transcript discovery
MMSEQ aims to quantify the abundance of known transcripts, and as such relies on the comprehensiveness of the transcriptome's annotation. It is usually possible to align a very large proportion of the reads to Ensembl transcripts (approximately 75% in the HapMap study using Ensembl version 56). However, samples may contain previously unobserved genes or isoforms. MMSEQ can in such cases work in tandem with transcript discovery methods by adding newly predicted isoform sequences to the reference transcript FASTA file and using it in the alignment and mapping steps of the MMSEQ workflow.
Modeling biological variability
The Poisson distribution captures technical variability arising in repeated sequencing experiments with the same biological sample. The true expression value is, in effect, fixed by the experiment, and the only source of variability arises from measurement error and mapping uncertainty. However, between biological replicates such as different individuals in the HapMap study, there is, additionally, variability of a biological origin. As has been previously reported, this results in expression values between replicates that show overdispersion, captured, for example, by a negative binomial distribution [21].
Here we have focused on the problem of estimating the posterior distribution of expression values independently per sample. Nevertheless, it would be possible to add a further level to our Bayesian model to capture overdispersion across samples flexibly. For example, if exchangeable Gamma priors are set on the μ t , a suitable negative binomial model can be induced.
Phasing with paired-end data
In this work, we have phased genotype calls obtained from SAMtools pileups - an approach that works well with both single and paired-end data. However, in the case of paired-end data, the haplotypes observed directly at multiple SNPs spanned by overlapping read pairs could be used to increase confidence in the phasing calls. Although incorporating this information would benefit phasing estimates only for some sets of SNPs, we believe it is a worthwhile area of future research. As phasing is a distinct step in our pipeline, improved methodologies can be integrated flexibly as they become available.
RNA-seq is a promising and rapidly developing technology that provides sequence and expression intensity information of a sample in a single experiment. We have presented a novel pipeline and fast, scalable methodology to estimate expression of diploid organisms at the haplotype, isoform and gene levels. This allows researchers to go beyond allele-specific expression analysis and assess imbalance between paternal and maternal copies of isoforms, which in turn may be compared to differential isoform expression between individuals. We have shown that our method is able to deconvolve the expression of transcripts on each of two X chromosomes from human males in a pooled dataset, and that it can be successfully applied to detect genomic imprinting and cis-regulated transcripts in mouse hybrids. Our method retains reads that emanate from junctions as well as wholly within exons, models alignments to multiple transcripts, potentially across genes, exploits insert size information in paired-end data to choose the best alignments and flexibly incorporates corrective models for non-uniform read sampling. The pipeline, the MMSEQ software and related documentation are freely available online [14].
Materials and methods
Expectation maximization
which converges to the ML estimate of μ t . To initialize the algorithm, we set μ(0) equal to , which is equivalent to distributing k i evenly between cells of X i where M it is one. For a given region i, the probability of reads being allocated to a given transcript depends only on the μ t and not on s i (as the region is the same length on all transcripts). Hence, the s i do not appear in the update steps.
Bayesian model and Gibbs sampling
Again, the s i are not needed as they are absent from the full conditionals.
TopHat settings
Gapped alignment to the genome is performed with TopHat. We use a GFF file (specified with -G) based on the Ensembl annotation. We set --no-novel-juncs, --min-isoform-fraction 0.0 and --min-anchor-length 3. The expected inner distance between mate pairs is specified with the -r switch.
SAMtools pileup settings
Genotypes output by SAMtools pileup were filtered using samtools.pl varFilter with default options and setting a minimum Phred-scaled probability of the genotype being identical to the reference ('SNP quality') threshold of 20.
Bowtie settings
Alignment to the transcriptome with Bowtie is performed with the -a --best switches, which ensure all the best alignments in terms of mismatches are produced. Additionally, we recommend using --strata to output only alignments with the minimum number of mismatches, although it currently has no effect on paired-end data. The minimum and maximum insert sizes should be set appropriately with the -I and -X switches respectively, as should --norc/--nofw for stranded protocols.
Utah residents with ancestry from northern and western Europe
expectation maximization
Genome Analyzer II
Gibbs sampling
- Haplo-isoform:
haplotype-specific isoform
Monte Carlo standard errors
maximum likelihood
pseudo-autosomal region
reads per kilobase per million mapped reads
single nucleotide polymorphism
University of California: Santa Cruz.
This research was supported by BBSRC grant BBG0003521. We thank William Astle for constructive comments on the statistical model.
Authors' Affiliations
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- Heap GA, Yang JHM, Downes K, Healy BC, Hunt KA, Bockett N, Franke L, Dubois PC, Mein CA, Dobson RJ, Albert TJ, Rodesch MJ, Clayton DG, Todd JA, van Heel DA, Plagnol V: Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum Mol Genet. 2010, 19: 122-134. 10.1093/hmg/ddp473.PubMedPubMed CentralView ArticleGoogle Scholar
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This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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Attacks on the Press | Philippines
Attacks on the Press 2009: Philippines
• Maguindanao massacre underscores deep-seated climate of impunity.
• Local and international groups mobilize to offer aid, seek justice.
29: Journalists slain in a politically motivated ambush, the single deadliest event ever recorded by CPJ.
In the deadliest event for the press ever recorded by CPJ, 29 journalists and two media support workers were ambushed and brutally slain on November 23 as they traveled in Maguindanao province with a convoy of people who intended to file gubernatorial candidacy papers for a local politician. In all, 57 people were killed in a shocking display of barbarism apparently motivated by political clan rivalries. The bodies were dumped in mass graves in a remote clearing in the town of Ampatuan.


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Proprietary DRMOther examples of proprietary malware
Nonfree (proprietary) software is very often malware (designed to mistreat the user). Nonfree software is controlled by its developers, which puts them in a position of power over the users; that is the basic injustice. The developers often exercise that power to the detriment of the users they ought to serve.
Here are examples of proprietary programs and systems that implement digital restrictions management (DRM): functionalities designed intentionally to restrict what users can do. These functionalities are also called digital handcuffs.
DRM is reinforced by censorship laws that ban software (and hardware) that can break the handcuffs. Instead of these laws, DRM itself ought to be illegal. Please support our campaign to abolish DRM.
Windows DRM files can be used to identify people browsing through Tor. The vulnerability exists only if you use Windows.
Chrome implements DRM. So does Chromium, through nonfree software that is effectively part of it.
HP's firmware downgrade imposed DRM on some printers, which now refuse to function with third-party ink cartridges.
Oculus Rift games now have DRM meant to prevent running them on other systems.
The "Cube" 3D printer was designed with DRM: it won't accept third-party printing materials. It is the Keurig of printers. Now it is being discontinued, which means that eventually authorized materials won't be available and the printers may become unusable.
With a printer that gets the Respects Your Freedom, this problem would not even be a remote possibility.
How pitiful that the author of that article says that there was "nothing wrong" with designing the device to restrict users in the first place. This is like putting a "cheat me and mistreat me" sign on your chest. We should know better: we should condemn all companies that take advantage of people like him. Indeed, it is the acceptance of their unjust practice that teaches people to be doormats.
Phillips "smart" lightbulbs have been designed not to interact with other companies' smart lightbulbs.
If a product is "smart", and you didn't build it, it is cleverly serving its manufacturer against you.
The Amazon Kindle has DRM. That article is flawed in that it fails to treat DRM as an ethical question; it takes for granted that whatever Amazon might do to its users is legitimate. It refers to DRM as digital "rights" management, which is the spin term used to promote DRM. Nonetheless it serves as a reference for the facts.
We refer to that product as the Amazon Swindle because of this and other malicious functionalities.
DRM in Windows, introduced to cater to Bluray disks. (The article talks about how the same malware would later be introduced in MacOS. That had not been done at the time, but it was done subsequently.)
DRM in MacOS. This article focuses on the fact that a new model of Macbook introduced a requirement for monitors to have malicious hardware, but DRM software in MacOS is involved in activating the hardware. The software for accessing iTunes is also responsible.
A further consequence of this malware is that users may have trouble playing videos on auxiliary large screens. (The article, from a publication whose name suggests it idolizes Apple, treats these restrictions as irreproachable.)
Adobe made "Digital Editions," the e-reader used by most US libraries, spy on the user for the sake of DRM.
DVDs and Bluray disks have DRM.
That page uses spin terms that favor DRM, including digital "rights" management and "protect", and it claims that "artists" (rather than companies) are primarily responsible for putting digital restrictions management into these disks. Nonetheless, it is a reference for the facts.
Every Bluray disk (with few, rare exceptions) has DRM—so don't use Bluray disks!


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How "fit" is your family? There was a time, within living memory, when "fitness" meant much more than sculpted abs and a strong heart rate. As recently as 70 years ago, it also referred more ominously to hereditary improvement of the "race" through selective breeding. Promotion of fitness in this sense, or "eugenics," was so widely and casually embraced during the first half of the 20th century that many of its ideas were enshrined in marriage and reproductive law. While today only the most hard-hearted would press for sterilizing the "feeble-minded" or preventing the mentally retarded from marrying, similar arguments are regularly made in favor of banning same-sex marriage.
According to The Science of Eugenics, published by the Eugenics Health Foundation in 1930, the term "unfit" covered enormous ground. It included anyone suffering from "nervous prostration, sick headaches, neurasthenia, hysteria, melancholia, St. Vitus' dance, epilepsy, syphilis, alcoholism, pauperism, criminality, prostitution and insanity. … nervous disorders, including certain forms of deafness, color blindness and other indications of defectiveness and degeneracy." Of course, eugenicists also considered "homosexuality" degenerate, an embarrassing blight on the family gene pool, something that "should be inhibited in the interest of civilization and the well-being of future generations," according to Dr. F.E. Daniel in 1893. By the end of the 1930s, eugenicists had pushed through a web of state laws prohibiting those they viewed as genetically inadequate from marrying. But since homosexual couples couldn't reproduce, no one went to the trouble of outright prohibiting that group of the "unfit" from marrying each other.
Until now. Some prohibitions on marriage among the "unfit" still linger, unenforced, on the books, but many have been repealed, thanks to the rise of the disability rights movement in the 1970s. For gay people, however, the fun is just beginning: the right-wing rhetoric of "marriage protection" employs the same logic and language used by proponents of eugenics in the early-20th century. And it's about time they be called on it.
Given the recent string of legal setbacks for same-sex marriage, advocates should reassess their strategies both in- and outside the courtroom. After all, the argument that gay people should be able to marry each other because they are full citizens under the law can be further advanced if we understand what same-sex couples share, legally and culturally, with others who have historically been prohibited from marrying. For that we must look to the unseemly history of genetic engineering in the US, in which it is apparent that denial of equal marriage rights is linked to America's dark eugenics past.
Medical madcapping
This desire to filter the breeding pool began in the heart of the industrializing cities at the end of the 19th century. As middle-class white people felt overwhelmed and frightened by the flood of lower-class immigrants pouring into the US, a determined group of social reactionaries — including many respected scientists and a surprising number of leading feminists interested in "family planning" — launched the eugenics movement to purge human "stock" of the "unfit." To quicken the "survival of the fittest," crusaders lobbied for legal reforms that would regulate marriage in such a way as to kill off, through attrition, socially and biologically undesirable groups.
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Bloody July: In just one month, six different State Supreme Courts have ruled against gay marriage. By Michael Amico
What is eugenics?
According to the second edition of Webster's International Dictionary, published in 1934, eugenics is "The science that deals with influences … that improve inborn or hereditary qualities in a series of generations of race or breed, esp. of the human race." In practice, that meant, among other things, seeking legislation to prohibit the "unfit" from marrying. In 1921, for example, New York State considered "An act to amend the domestic relations law, in relation to the prevention of hereditary blindness" that proposed giving judges power not to certify marriage between the blind if "by reason and the nature of such visual defects the children of such marriage might become blind and thereby be a charge upon the public."
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text: _DSC9709 by Tim Mar on 17/01/2012 add comment 6 views facebookTwitter Google + TumblrEmail facebookTwitter Google + TumblrEmail The author Tim Mar Owner and co-founder of BombSquadSF. Also a photographer for Levis Strauss, Fatlace, Blackscale, and more. Hope you guys enjoy my photos! you might also like 40 is the new 4ever Vintage Electric To Release Limited Edition Emory Outlaw MVMT Gets Ready For Spring Break with New Collection of Eyewear Would You Airbnb at Drizzy's? The Outlier's Guild Custom Moto Show in Downtown LA on May 6 Leave a Response Cancel reply CommentName Email


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By Southern Advocate
Hickory Flat native Lamar Sanders began a new adventure when he moved to Japan in October.
"There's a lot of high fashion and I'm really into fashion right now," said Sanders during a recent interview.
Unfortunately, at 6-foot-7, Sanders can only admire the fashions there. In a country where the average male height is 5-7, most stores don't have clothing on the rack in his size.
Sanders' unusual stature isn't the largest thing about his experience in Japan, though. He's there to live the fulfillment of a pretty big dream – playing professional basketball. Sanders has been playing basketball for as long as he can remember. He's been breaking records and earning honors for almost as long.
A standout player at Hickory Flat High School, averaged 29 points per game and 14.7 rebounds per game his senior year. He scored a career-best 62 points in one game, breaking state records, and was named first team All-State as a junior and senior.
At Northwest Mississippi Community College and Lamar University, he continued to stand out.
Sanders is no newcomer to playing professional basketball, either. He began his professional career in 2008, when he signed with a professional basketball team in Spain. Since then, he has played for the Southeast Texas Mavericks and the Jacksonville Giants. Now, he's continuing to live his dream in Tokyo, playing for the Tukuba Daytricks.
And he's playing well. Sanders had a game-high 30 points and 16 rebounds in Monday's 80-76 loss to the Hitachi Cable Bulldogs. In the latest update, he's second in scoring in the Japan Basketball League 2 with a 21.4 scoring average and leads the league in rebounding at 16.9 per game.
He's also second in the league in field goal percentage (.691), third in blocked shots (1.28), third in dunks (1.1) and sixth in steals (1.6).
Despite Monday's loss, his team leads the JBL2 Eastern Division with a 13-5 record.
Sanders was an Eastern Division Player of the Month in October.
The best thing about his latest venture, he said, is getting to see the world. "I'm doing something I never thought I'd be doing," he said. "Especially coming from the small town of Hickory Flat."
In Japan, he says the game moves faster and is played at a high tempo, but is essentially the same. "Basketball is basketball – I've been doing that since I can remember," he laughs.
New lessons
Basketball may be the same in Japan, but little else is. For Sanders, some of the biggest adjustments have been adjusting to the food and the language. He's taking classes to learn Japanese and has a translator for work.
He knows a few basic words at this point and is finding ways to compensate. For example, when ordering food, most places have photographs on the menu.
The most difficult part, though, is being away from the people he loves who are still in America.
"I'm surely blessed to be in this situation – I've come a long way," he said. "I never thought I'd make it this far, just excited about being a professional basketball player."
In Japan, as Sanders adjusts to a new way of life, he named one person as absolutely indispensable – his translator, Arimoto J. Hasegawa. "If it weren't for him, I'd be back in the States. He's phenomenal, does a good job and I appreciate him so much," Sanders said. "He makes life for me in Japan really easy."
His girlfriend, Lauren Holdorff, is a big part of his support system, too. "She keeps me motivated and helps me with my dreams," he said. "She's more than I could ever ask for."


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May 22, 2013
Fort HealthCare is holding the third annual Camp 911, a one-day program focusing on safety, prevention techniques and health and wellness for children entering fourth through sixth grades in the upcoming 2013-2014 school year. Camp 911 will be held Wednesday, June 12 and Thursday, August 22 from 7:30 a.m. to 4:30 p.m. at Fort Memorial Hospital. The registration fee is $15 per child. Camp 911 will provide children the knowledge, skills and confidence to protect themselves, react safely in emergency situations and increase awareness of health and wellness. Community agencies like the Jefferson County Sheriff Department, Jefferson County K-9 Unit, Med Flight and Ryan Brothers Ambulance will be participating. Additional activities will include CPR and First Aid, fire safety, safety at home, bike safety, smoke house simulation, 911 call simulation, exercise course, relay races, activity fair and more!
Participants will receive a t-shirt and beverages, and snacks and lunch will be provided. Visit FortHealthCare.com/Classes to register online. Space is limited to 70 participants per session and registrations are based on a first-come, first-served basis. Camp 911 is sponsored by Fort HealthCare, Wetzel Builders, Kutz Dairy and Fredrick Farms.


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do not use off_t in headers - largefile sensitivity bugs!
Through a discussion on alt.os.linux.mandrake, I had to notice that every library has a risk of being broken when using the system off_t type in its exported interfaces, including structures and function synopsis.
The point comes from the fact that systems like linux and solaris are "largefile sensitive" - a -D_LARGEFILE_SOURCE will shift the "off_t" type from being a 32bit entity into a 64bit entity. This will make for a nice and pretty callframe mismatch.
A autoconf'ed lib 'centric treatment of the topic is given in:
Grepping a bit through files on my system, I did notice that even zlib/gzip is affected (and only by luck it is not triggered) and kdelib header files (in kio) has off_t as well. Bug reports were filed to the respective projects.
People should worry and learn about this problem area sooner than later


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What's the best way to announce a pgp / gpg keysigning party ?
I'm organizing a Key-signing party - I've contacted people on biglumber.com. I'll probably post the event on upcoming.org. I will contact the local LUG. What else should I do to get more people to attend ?
Syndicated 2012-01-16 10:38:33 (Updated 2012-01-16 10:40:34) from Ludovic's weblog


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New York City, New York 10022
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A. Harrison Barnes is a well-known attorney throughout the United States. As a member of the Malibu community, Harrison is committed to serving the needs of Malibu residents and businesses in legal matters.
Benjamin P. Smith is a partner in Morgan Lewis's Litigation Practice. He is a trial lawyer with a particular focus on high-stakes disputes in the biotechnology, medical device, and internet industries.


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With the coming controversies of Christmas I figure this should be a good pre- Holiday read.
History Matters
Misusing History
Thomas Jefferson's "wall of separation" metaphor allowed the Supreme Court to redefine church-state law and policy—and not necessarily in a good way.
Daniel Dreisbach | posted 11/12/2008 02:13PM
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Originally a restriction on the civil government's powers, the First Amendment has been reinterpreted to grant power to the government to define and, ultimately, restrict the place of religion in society. Herein lies the danger of this metaphor. Today people frequently invoke the "wall" to separate religion from public life, thereby promoting a religion that is essentially private and a civil state that is strictly secular.
The "high and impregnable" wall constructed by the modern Court inhibits religion's ability to inform the public ethic, deprives religious citizens of the civil liberty to participate in politics armed with ideas informed by their spiritual values, and infringes the right of religious communities and institutions to extend their prophetic ministries into the public square. Jefferson's figurative barrier has been used to silence the religious voice in the marketplace of ideas and to segregate faith communities behind a restrictive wall.
Those who criticize modern constructions of the wall are not necessarily supporting a religious establishment. Rather, these critics contend that the First Amendment requires that religion and religious perspectives must be allowed to compete in the public sphere, without government inhibition, on the same terms as their secular counterparts. By its very nature, however, a high wall does not permit this.
The use of Jefferson's metaphoric wall to exclude religion from public life is at war with our cultural traditions insofar as it shows a callous indifference toward religion. It also offends basic notions of freedom of religious exercise, expression, and association in a pluralistic society. Unfortunately, the Supreme Court's "high and impregnable" wall has redefined First Amendment principles, transforming a bulwark of religious liberty into an instrument of intolerance and censorship.
Daniel L. Dreisbach is professor of justice, law, and society at American University and author of Thomas Jefferson and the Wall of Separation between Church and State (2002).
Copyright © 2008 by the author or Christianity Today International/Christian History & Biography magazine.
Click here for reprint information on Christian History & Biography.
Entire article here: http://www.christianitytoday.com/ch/...nghistory.html