text:
Victor Duvanenko is a long-time contributor to Dr. Dobb's. He can be contacted at [email protected]
We've reached the tenth part of this series on algorithm performance. It seems like a nice arbitrary spot to take inventory and reflect, before continuing on the journey of the next nine. Algorithms that were developed and studied fit into two categories: sequential and parallel.
Sequential Algorithms
We started out by implementing and studying performance of sorting algorithms. Sequential algorithms were first, such as Insertion Sort and Selection Sort, followed by development of In-Place Binary-Radix Sort, In-Place MSD N-bit-Radix Sort, Stable MSD N-bit-Radix Sort and Counting Sort, along with development of Parallel In-Place Radix Sort and Parallel Counting Sort.
To visualize and compare performance of various sorting algorithms, we used 2D logarithmic plots, which enabled comparison across 8 orders of magnitude — from arrays of 10 elements to arrays of 100 Million elements. Exponents in performance characteristics became clearly visible as differing slopes &mdash e.g. O(n2) has a slope of two, whereas O(n) has a slope of one, and O(nlgn) has varying slope that is much closer to one than to two.
The hybrid algorithm approach (similar to introsort and STL sort) was used to improve performance of several algorithms. This approach combined Insertion Sort, which performs well for very small array sizes, with the target sorting algorithm. The combination yielded higher performance than using a pure sorting algorithm. Insertion Sort is especially useful when combined with a recursive divide-and-conquer sorting algorithm to handle small termination cases. Insertion Sort is also in-place, which matches well to in-place algorithms.
In-place MSD N-bit-Radix Sort was developed — a potentially new algorithm. It's a linear-time algorithm of O(n) . The hybrid implementation outperforms STL sort by several times for arrays of 8, 16, 32 or 64-bit integers. It is of comparable performance to Intel's IPP Radix Sort, which is not in-place, requiring an external array of same size as the input array. However, the In-Place MSD N-bit-Radix Sort is not stable (which is not an issue when sorting arrays of numbers, but may be an issue for certain use cases). This algorithm was extended to sort arrays of signed integers. A stable MSD N-bit-Radix Sort was also developed, which sadly traded in-place for stability.
The Counting Sort algorithm was developed. This high performance linear-time O(n) sorting algorithm, with low constant factors and favorable memory access patterns, is limited to cases where the range of values is small (which made it a perfect match for use inside Radix Sort). It was shown to perform well for arrays of 8, or 16-bit numbers, outperforming STL sort by over 20X. Data type adaptive sorting could be developed to detect arrays of 8 or 16-bit elements (or small ranges) and select Counting Sort to harness this level of performance. It was extended to handle arrays of signed or unsigned numbers without performance degradation.
Various input data patterns were used to test algorithm performance, such as incrementing, decrementing, constant, and random values using several algorithms. The quality of these random number generation algorithms was examined visually. Using analysis tools provided by NIST exposed weaknesses in one of the random number generators under certain usage conditions, which resulted in only 4 thousand unique values within 100 million 32-bit values generated, as well as failing most of NIST tests. Algorithm performance sensitivity to input data variation was also explored, showing some algorithms to be oblivious to input data variations, while others (such as STL sort) took full advantage of less variation, accelerating by over two orders of magnitude.
When comparing performance of algorithms, using the worst-case input distribution specific to each algorithm is a powerful evaluation method. Measurements showed that In-Place Radix Sort is sensitive to input data that is constant, but STL sort performs worse with random inputs. Under these worst-case to worst-case comparisons, In-Place MSD N-bit-Radix Sort outperformed STL sort by several times. Yet, it is unknown whether these truly are worst-case inputs for each of the algorithms.
Sorting algorithms from Intel's IPP library (a suite of Radix and other sorts for numeric arrays) as well as STL sort (stable and not) were used for comparison.


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Search Will Air as a Five-Episode Web Series Competition on PriceIsRight.com and Youtube.com/PriceIsRight, With Viewers Voting Online for the Winner
THE PRICE IS RIGHT is holding its first-ever search to find a male model. The search will air as a five-episode web series competition on PriceIsRight.com and Youtube.com/PriceIsRight in late September. The winner, who will be chosen by viewers, will win a one-week modeling gig on the game show.
The search will begin with an open casting call in Los Angeles on Thursday, August 30, when the male model hopefuls will be interviewed and judged by the show's female models and show producers on qualities such as their verbal skills, posing and ability to properly showcase a product. Contestants who are selected to move on will participate in a series of challenges designed to reveal who has the best on-camera presence and modeling skills. The judges will eliminate contestants after each challenge, but at certain points, one of the two contestants who finish in the bottom of a challenge may have the chance to win their way back into the competition. At the end of the web series, up to six contestants will remain, where it will be up to the viewers to determine the winner.
Following the competition, the finalists will be revealed during the Friday, Sept. 28 episode of THE PRICE IS RIGHT. Viewers will have the opportunity to vote online for their favorite model at priceisright.com through Thursday, Oct. 4. The winner will begin their week-long modeling gig on THE PRICE IS RIGHT on Monday, Oct. 15.
Following is the information for the open call:
Thursday, August 30, 10:00 AM - 2:00 PM
KCBS Studios
4024 Radford Avenue
Studio City, CA 91604
Go to priceisright.com for official rules and eligibility.
THE PRICE IS RIGHT, the longest-running game show in television history, is hosted by Drew Carey. Produced by FremantleMedia North America, THE PRICE IS RIGHT is broadcast weekdays (11:00 AM-12:00 Noon, ET; 10:00-11:00 AM, PT) on the CBS Television Network.
Website: http://www.cbs.com/daytime/the_price_is_right/
Facebook: http://www.facebook.com/ThePriceIsRightCBS
Twitter: http://twitter.com/TPIR_CBS
Drew Carey on Twitter: https://twitter.com/TPIRHost
CBS Twitter: http://twitter.com/CBSTweet

subset: commoncrawl


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Two friends, one jumbled, well-intentioned message, and a whole lot of Internet buzz. Brad Paisley's new single "Accidental Racism" has fans and critics scratching their heads over what exactly the country crooner and collaborator LL Cool J are trying to get at in the pseudo-apologetic track, which was leaked online just ahead of Paisley's album release on Tuesday, April 9.
The song, which starts off with a series of forlorn guitar rifts, initially seems to be an earnest attempt to address issues like racism, the Confederacy and slavery. But upon closer listen, there actually isn't much of an apology in the lyrics at all.
PHOTOS: Academy of Country Music awards 2013
"To the man that waited on me at the Starbucks down on Main, I hope you understand," the song begins, "When I put on that T-shirt, the only thing I meant to say is I'm a Skynyrd fan/ The red flag on my chest somehow is like the elephant in the corner of the South."
Paisley, 40, then goes on to detail how even though he's apologetic for what his ancestors may have done in the past, "Our generation/ Didn't build this nation," and therefore he is not actually guilty of being a true racist.
"I'm just a white man/ Living in the southland," he croons over the groove of the song, later adding that "I try to put myself in your shoes/ That's a good place to begin/ But it ain't like I can walk a mile in someone else's skin."
At one point during the song, Paisley's pal LL Cool J offers his two cents, rapping from his point of view as a "do-rag" wearing, "gold chain" donning black man who similarly wants to break past stereotypes.
"If you don't judge my do-rag, I won't judge your red flag," he raps on the track as Paisley continues to bemoan the difficult internal struggles of being "proud of where I'm from but not everything we've done."
The "Whiskey Lullaby" singer defended his decision to pen and record the controversial song, however, telling Entertainment Weekly that the track is not a "stunt."
"I'm doing it because it just feels more relevant than it even did a few years ago," he said of why he chose to tackle such hot-button issues in the song. "I think that we're going through an adolescence in America when it comes to race. You know, it's like we're almost grown up. You have these little moments as a country where it's like, 'Wow things are getting better.' And then you have one where it's like, 'Wow, no they're not.'"
Paisley also pointed to Hollywood's hits Lincoln and Django Unchained as reasons to bring up the oft-uncomfortable conversation.
"I just think art has a responsibility to lead the way, and I don't know the answers, but I feel like asking the question is the first step, and we're asking the question in a big way," he continued. "How do I show my Southern pride? What is offensive to you? And he kind of replies, and his summation is really that whole let's bygones be bygones and 'if you don't judge my do rag, I won't judge your red flag.'"
"We don't solve anything, but it's two guys that believe in who they are and where they're from very honestly having a conversation and trying to reconcile."
So tell Us, do you think Brad Paisley's song is offensive or just misunderstood?
This article originally appeared on Usmagazine.com: Brad Paisley, LL Cool J Spark Controversy With New Song "Accidental Racism"


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Someone should make a musical about the remaking of Smash between its first and second seasons. Let's call it Phantom of the Rewrite.
Or maybe The (New) Producers, seeing how NBC replaced the original creator/showrunner in hopes of calming this elaborate backstage drama's own behind-the-scenes creative turmoil, which manifested on screen in turgid and oft-ridiculed soap opera between the splashy production numbers (which are still mostly terrific). Smash 2.0 (Tuesday, 9/8c) wastes no time addressing, while slyly commenting on, the show's problem spots, many involving Debra Messing's character, insecure lyricist-librettist Julia Houston. Her dull husband, cloddish son and needy lover? History. Her hideous scarves? Mocked. Also soon to be gone. Along with reviled characters like the scheming, lurking Ellis and Karen's cheating ex, Dev.
And in the most telling in-joke, when the out-of-town reviews come in for the show-within-the-show Bombshell, what gets the most savage notices? The writing! How meta of Smash.
Julia's still a mess, though in a nod to Messing's previous hit Will & Grace, she moves in with her gay composing partner, Tom (scene-stealer Christian Borle). It's one of several smart choices as Smash expands its focus beyond the world of Bombshell, a gossip magnet thanks to financial/legal setbacks and a sexual-harassment scandal involving its cad of a director, Derek Wills (Jack Davenport as the show's most entertaining character).
Taking a page from the old Mickey-and-Judy "let's put on a show" playbook, Smash introduces its winsome ingénue Karen (Katharine McPhee) to a headstrong young songwriter with hip Rent ambitions (rising star Jeremy Jordan, who headlined two real Broadway musicals last year). This subplot, like much of Smash, is cheesy and corny, but works when the impassioned singing starts. Which, for a musical drama about musicals, is what matters most. Smash has a ways to go to earn its standing O, and the hate-watchers are still probably gonna hate. Without a sure-fire lead-in from The Voice this season, the ratings might turn out to be more suitable for off-Broadway, but at least the sour notes are fewer and farther between.
Want more TV news and reviews? Subscribe to TV Guide Magazine now!
THEIR LIPS ARE SEALED: But for how long, as Fox's New Girl (9/8c) dives headlong into the hilariously awkward aftermath of last week's kiss between Jess and Nick — an inevitable twist that we all saw coming (thanks, promos!), and yet their impulsive and lingering smooch resolves nothing. Nick stays busy passive-aggressively perfecting his panicked backwards moonwalk every time Jess comes near, and she's conflicted about how much to spill to her smitten swain Sam (David Walton, who's been a real bonus this season). As they comically banter about how much the kiss means, if it means anything, it all comes to a head at an Indian marriage convention where Cece is shopping for new husbandly prospects, naturally prompting a turbaned Schmidt to crash the party. (The way Schmidt uses "Calcutta" in a threat to other suitors is especially inspired.)
The Mindy Project's title character would love these rom-com shenanigans, but in a week-early Valentine's themed episode (9:30/8:30c, Fox), she's got her own dilemma: a double date involving her latest guy (B.J. Novak), whose female BFF she sets up with Danny, and their instant connection throws off her own mojo.
THE HILLS ARE ALIVE: In the Kentucky of FX's marvelous Justified (10/9c), with bad apples who get in the way of Raylan and Boyd's separate (but equally perilous) search for the long-missing Drew Thompson. There's a bonanza of guest stars this week, including The Following's Natalie Zea in an all-too-brief return as Raylan's expecting ex Winona, another welcome cameo by Patton Oswalt as the overeager Constable Bob, plus Mike O'Malley as an enforcer from Detroit and Gerald McRaney adding to his gallery of wily coots.
ALL BETS ARE OFF: For Deputy Jack Lamb (Jason O'Mara) of CBS' Vegas (10/9c), who's frantically cleaning up the mess that left his girlfriend's mobster father dead in last week's violent confrontation. As a lounge singer (Jersey Boys Tony winner John Lloyd Young) symbolically croons "Let's Face the Music and Dance," Jack has to decide whether to cover up his involvement or come clean to his sheriff brother and the grieving Mia (Sarah Jones). That's a juicy enough story to make this week's self-contained subplot (about a friend of Dixon's caught up in a car-theft ring) even more regrettable and tedious than usual.
REMEMBER WHEN: PBS' enjoyable Pioneers of Television (check tvguide.com listings) ends its winter run with a look back at a mostly vanished art form: the network TV miniseries, for which you'd think last year's all-star blockbuster Hatfields & McCoys on History might have revived some interest. Those really were the days when a network like ABC would devote an entire week — I was there every night, including on my birthday — to a ratings-shattering epic like Roots, which is remembered by its stars. Also featured: Rich Man, Poor Man, one of the first "novels for TV," and marking its 30th (!) anniversary, the lushly romantic The Thorn Birds.
THE TUESDAY GUIDE: Cyber-terrorism is a hot topic: front page of The New York Times on Monday, the driving motivation behind last week's villain on Person of Interest, and now on CBS' NCIS (8/7c), the team goes after a super-hacker who could help them find the world's most-wanted cyber-terrorist. ... Who do we have to thank for all of this high tech? The early mavericks of Silicon Valley, the subject of a 90-minute American Experience on PBS (check tvguide.com listings) which focuses on Intel founder Robert Noyce, who led his "Traitorous Eight" scientists into an era of invention, including the integrated circuit, that changed pretty much everything about modern life. ... On USA Network's White Collar (10/9c), the underused Diahann Carroll finally gets to work her celebrated pipes, singing two numbers at the fabled Cotton Club as Neal and Peter's latest forgery/money-laundering investigation takes them into the world of New York jazz.


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Double & King Size BedsQueen Size Double Beds | King Size Beds | Contemporary Beds
Double & King Size Beds
Usually, children are used to sleeping in single beds and approach double beds only when they grow up. It is an important passage of our lives. Double beds do not only symbolise life as a couple. Being single and having a double, king size or even a super king size bed means a lot of comfort. Today, in fact, many children and young people who live with their parents are used to sleep in double beds. Everyone should, of course, shape their bedroom according to their own tastes and needs - for example, if you like to study at the desk in your bedroom, then you may want to have a single bed to save some space (unless, of course, you have a really big room!), but if you feel like a double bed is the best place where reading, studying and relaxing, then go for it!
If, instead, you have just moved in with your partner or you have been together for a long time but want to replace your old bed, we have a very wide range of different beds that you may want to consider. If you have a soft spot for wrought iron metal beds, we have a whole section about them and our main supplier is Cosatto. They are elegant, smart and unique in their original design. If you are particularly interested in this type of bed, we strongly suggest you to have a look at the Wrought Iron Beds section, where you'll find many different beds with amazing names such as Incanto, Diva and so on, all by Cosatto. If instead you want a very big bed but you also need to save some space and eventually do some storage, then there is a great solution for you: go to the Storage Beds section and find the best wooden fram bed for you! These beds have beautiful designs and they also provide a lot of storage. We sell a wide range of storage beds, created by various Italian designers. Have a look to see if there is any bed that may interest you.
If instead you are not in a urge to save some space and you just want a high-quality, elegantly designed bed, then there are also a lot of other opportunities that you can't miss. For example, we do really love the bed Segmento by Veneran, It has a smart, modern design and it is also available in different sizes according to your tastes and needs. You can choose between a wide range of colours and make it perfectly in style with the rest of your room. Interestingly enough, there is also a wide range of upholstered beds that you may choose. They can be made of fabric, eco-leather or leather, and can be of different dimensions. Remember, the bed is such a centrepiece for your bedroom and such an important piece of furniture for your house, that you need to choose it carefully and do as many experiments as you want. This is a very important decision. Of course, you may have different priorities or different tastes, both in terms of comfort and aesthetics, but what we really want to guarantee you is that we are of course available to help you with every request you may have about the different beds, dimensions, designs and colours that you will find in our catalogue.


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Includes national and international spectrum allocations,
wireless service registrations and equipment configuration
parameters plus measured or reported spectrum occupancy,
cleaned raw data, and more.
Contact us
to discuss integrating Key Bridge technologies into your own solutions.
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All documents shown here are included in the seminar for instant download
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available on CD and for instant download. All reference material as
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Comparing GLP with GMP
Learn about similarities and differences
and when to apply one or the other
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Answers to the questions above will be
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During the seminar, the speaker will present strategies and give
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MMMOOO Essential
It's a time to say goodbye to 2014, the year we shifted our business focusing. We decided to stop our main force in personal mobile app development and provision.
So welcome the 2015! In the new exploring and incubation period, MMMOOO mainly cover 3 areas: Premium Outsourcing; Early Stage Investing; Device Sales.
Premium Outsourcing: as the most famous ISV, we will do outsourcing in mobile app(iOS, Android, Windows and BlackBerry), H5, CMS, premium UI/UX, professional coding, passionate communication and service.
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We embrace the fast growing & challenging mobile app industry, we are right here to Enrich Your Mobility! Our business will focus on killer apps, you can expect more of MMMOOO in the 2014. Also it's our big passion to help enterprises to develop mobile app & server client, we did another 10+ project for leading content providers.
MMMOOO develop and port cross platforms apps worldwide & locally: Nokia, BlackBerry, Windows Phone, iOS and Android. We are top achiever in worldwide of Nokia and BlackBerry, and leverage our experience & passion in iOS, Android and Windows.
Shanghai Jibiao, MMMOOO's parent company, also provide one-stop solution for enterprise from coding to present service to end user, smoothly and steady! In the past, we were the authorized vendor to design and host the media service of smartphone for 2010 Shanghai World Expo and help dozens of industry leader's to develop mobile apps.
MMMOOO is the international trademark and brand of Shanghai Jibiao Info Tech Co., Ltd. We embrace the DNA: a built to last enterprise.


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This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Off-label workflow to simply call differences in two samples
Given my years as a biochemist, if given two samples to compare, my first impulse is to want to know what are the functional differences, i.e. differences in proteins expressed between the two samples. I am interested in genomic alterations that ripple down the central dogma to transform a cell.
Please note the workflow that follows is NOT a part of the Best Practices. This is an illustrative, unsupported workflow. For the official Somatic Short Variant Calling Best Practices workflow, see Tutorial#11136.
To call every allele that is different between two samples, I have devised a two-pass workflow that takes advantage of Mutect2 features. This workflow uses Mutect2 in tumor-only mode and appropriates the
--germline-resource argument to supply a single-sample VCF with allele fractions instead of population allele frequencies. The workflow assumes the two case samples being compared originate from the same parental line and the ploidy and mutation rates make it unlikely that any site accumulates more than one allele change.
First, call on each sample using Mutect2's tumor-only mode.
gatk Mutect2 \ -R ref.fa \ -I A.bam \ -tumor A \ -O A.vcf gatk Mutect2 \ -R ref.fa \ -I B.bam \ -tumor B \ -O B.vcf
Second, for each single-sample VCF, move the sample-level
AF allele-fraction annotation to the INFO field and simplify to a sites-only VCF.
This is a heuristic solution in which we substitute sample-level allele fractions for the expected population germline allele frequencies. Mutect2 is actually designed to use population germline allele frequencies in somatic likelihood calculations, so this substitution allows us to fulfill the requirement for an
AF annotation with plausible fractional values. The terminal screenshots highlight the data transpositions.
Third, call on each sample in a second pass, again in tumor-only mode, with the following additions.
gatk Mutect2 \ -R ref.fa \ -I A.bam \ -tumor A \ --germline-resource Baf.vcf \ --af-of-alleles-not-in-resource 0 \ --max-population-af 0 \ -pon pon_maskAB.vcf \ -O A-B.vcf gatk Mutect2 \ -R ref.fa \ -I B.bam \ -tumor B \ --germline-resource Aaf.vcf \ --af-of-alleles-not-in-resource 0 \ --max-population-af 0 \ -pon pon_maskAB.vcf \ -O B-A.vcf
- Provide the matched single-sample callset for the case sample with the
- Avoid calling any allele in the
--germline-resourceby setting
--max-population-afto zero.
- Maximize the probability of calling any differing allele by setting
--af-of-alleles-not-in-resourceto zero.
- Prefilter sites with artifacts and cross-sample contamination with a panel of normals (PoN) in which confident variant sites for both sample A and B have been removed, e.g. with
gatk SelectVariants –V pon.vcf -XL AandB_haplotypecaller.vcf –O pon_maskAB.vcf.
Fourth, filter out unlikely calls with FilterMutectCalls.
gatk FilterMutectCalls \ -V A-B.vcf \ -O A-B-filter.vcf gatk FilterMutectCalls \ -V B-A.vcf \ -O B-A-filter.vcf
FilterMutectCalls provides many filters, e.g. that account for low base quality, for events that are clustered, for low mapping quality and for short-tandem-repeat contractions. Of the filters, let's consider the multiallelic filter. It discounts sites with more than two variant alleles that pass the tumor LOD threshold.
- We assume case sample variant sites will have a maximum of one allele that is different from the
--germline-resourcecontrol. A single allele call will pass the multiallelic filter. However, if we emit any shared variant allele alongside the differing allele, e.g. for a heterozygous site without ref alleles, then the call becomes multiallelic and will be filtered, which is not what we want. We previously set Mutect2's
--max-population-afto zero to ensure only the differing allele is called, and so here we can rely on FilterMutectCalls to filter artifactual multiallelic sites.
- If multiple variant alleles are expected per call, then FilterMutectCall's multiallelic filtering will be undesirable. For example, if changes to allele fractions for alleles that are shared was of interest for the two samples derived from the same parental line, and Mutect2
--max-population-afwas set to one in the previous step to additionally emit the shared variant alleles, then you would expect multiallelic calls. These will be indistinguishable from artifactual multiallelic sites.
This workflow produces contrastive variants. If the samples are a tumor and its matched normal, then the calls include sites where heterozygosity was lost.
We know that loss of heterozygosity (LOH) plays a role in tumorigenesis (doi:10.1186/s12920-015-0123-z). This leads us to believe the heterozygosity of proteins we express contributes to our health. If this is true, then for somatic studies, if cataloging the gain of alleles is of interest, then cataloging the loss of alleles should also be of interest. Can we assume just because variants are germline that they do not play a role in disease processes? How can we account for the combinatorial effects of the diploid nature of our genomes?
Remember regions of LOH do not necessarily represent a haploid state but can be copy-neutral or even copy-amplified. It may be that as one parental chromosome copy is lost, the other is duplicated to maintain copy number, which presumably compensates for dosage effects as is the case in uniparental isodisomy.
This article is awesome! I do have a question now that I read through this a bit. I guess I am just not fully understanding the --germline-resource flag. Based upon the commands in this article, where is the Baf.vcf or Aaf.vcf being generated? I understand it's purpose and function but I just don't how to accomplish this on the commandline.
Hi @JmeAlena,
Thank you!
I do some hackery to reformat the data into these files. I'm pretty sure there are better ways so I left these details out.
What I do involves Excel and is as follows. Please do share any better approaches.
[1] Convert VCF data to table format using VariantsToTable.
gatk VariantsToTable \ -V A.vcf \ -F CHROM -F POS -F ID -F REF -F ALT -F TLOD \ -GF GT -GF AF \ -O A.table
[2] Modify
A.tablein Excel, e.g. using the
Don't forget to add the
#in front of
CHROM. Copy-paste column in-column as values, then remove/modify columns to make a VCF format file. Copy-paste contents to a text editor, e.g. that has preferences set to remove trailing white spaces, and save as text file
[3] Modify the VCF header.
Subset out the header then use nano to modify.
cat A.vcf | grep '##' > A.header nano A.header
Manually change (i)
INFOand (ii) use
kto delete unnecessary lines, etc.
[4] Concatenate header and body.
cat A.header Aaf.table > Aaf.vcf
[5] Validate file.
gatk ValidateVariants -V Aaf.vcf
Awesome! I am going to give it a try and I'll let you know how it goes. Thank you!
Hi! Sorry to bother you all again but I am setting up this pipeline to work for my data and I was curious if the panel of normals (PoN) file was necessary to run the program.
To recap what I am doing....
I am using clonal plant lineages to detect accumulation of somatic mutations as discussed in this forum. I want to basically obtain any unique SNVs among 12 samples of cloned plants exposed to differing selective pressures. So for example, a SNV might be present in some but not all. I technically have a control but mutation accumulation cannot be ruled out in these samples and must be analyzed as well.
I was curious if I do not have a model organism with known or confident sites, should I provide a PoN or can I leave this flag out? It appears that this flag has been created for those doing cancer research and I am not sure if it is applicable to my research. If it is required, how would you recommend I build and filter this type of vcf in my case?
With further consideration and thought, I have decided to take your advice one building the --germline-resource vcf but then analyzing the control samples with a treatment --germline-resource so that I get individual outputs for all files (I know it may seem a little funky)....
"If you follow the Mutect2 tutorial sans a matched normal BAM, then for the --germline-resource you can provide a callset representing the control group. This germline resource can use actual allele frequencies representing the control group samples. You would analyze each of the test group's samples against the germline resource in independent Mutect2 runs."
That all being said, how would this affect the creation or requirement of the PoN vcf? And how do the germline resource and PoN differ in the outcome?
No bother at all. Your questions are what the forum is for, and you should know that your courage to ask helps others who read.
curious if the panel of normals (PoN) file was necessary to run the program.
Technically, the tool does not require it.
Scientifically, I should think you would want it. Please see the paragraph that starts with "The panel of normals helps filter systematic artifacts of sequencing." in this document as to why. I imagine it would be easy for you to construct a panel from your current samples. Remember the PoN retains variants present in two or more samples as called by Mutect2. If you think the chances of a mutation arising in the same site in two samples is somehow higher for your case, then you can revert back to making the PoN the GATK3 way, which allows you to set the number of samples the retained sites must share, e.g. three or four instead of two.
To reiterate, any rare mutation analysis involving short read sequencing technology should be keen on incorporating a panel of normals to exclude artifacts of sequencing. The organism at hand should not be a factor in this decision. Actually, we know GRCh38 is one of the better reference genomes available, where the reference was tweaked to minimize uneven mapping and other empirical artifacts. I do not know the state of the quality of other reference genomes, but if they are less than GRCh38, then data mapped to such genomes, assuming similar quality of reads, benefit even more from using a PoN.
Section 2 of Tutorial#11136 outlines the two steps to create a PoN using GATK4. Section 1 of Tutorial#9183 outlines the steps to create a PoN using GATK3, which is where you can change the minimum number of samples a variant is observed in to be included in the PoN.
I was curious if I do not have a model organism with known or confident sites, should I provide a PoN or can I leave this flag out? It appears that this flag has been created for those doing cancer research and I am not sure if it is applicable to my research. If it is required, how would you recommend I build and filter this type of vcf in my case?
Remember that germline calling with HaplotypeCaller has different criteria for passing calls than somatic calling with Mutect2. You can run HaplotypeCaller on your cohort of samples and filter using recommended filtering parameters (hard filtering or VQSR) for confident germline variant sites. If you have a database of commonly germline variant sites for your organism, then you should definitely take advantage of it towards determining which of your cohort calls are confident (using VQSR). The germline callset will differ from the somatic calls you get with Mutect2, given somatic calling must account for fraction purity and heterogeneity common in cancer samples. Here you leverage the germline callset towards assessing the cutoff for variant inclusion in the PoN.
With further consideration and thought, I have decided to take your advice one building the --germline-resource vcf but then analyzing the control samples with a treatment --germline-resource so that I get individual outputs for all files (I know it may seem a little funky).... That all being said, how would this affect the creation or requirement of the PoN vcf? And how do the germline resource and PoN differ in the outcome?
You use the
--germline-resourceargument to provide the matched sample's Mutect2-called variant sites against which you want to contrast variant alleles. This will call all contrastive variants, some of which are likely artifacts. The PoN allows you to filter the artifactual sites. In the tutorial PoN, I do a hand-wavy approximation of masking germline sites in the PoN. I should think the resolution of this is dependent on how you determine which sites are truely germline variant sites. Towards this, the GATK offers VQSR (recommended), hard filtering guidelines and soon (in beta) a deep learning approach to variant filtering called GATK4 CNN.
I hope this clarifies things for you.
P.S. I have numbers to base my above comments on. The PoN filters a surprising amount of calls and I think it more likely these are artifacts than mutations of interest. But don't just take my word for it. You should do a comparison +/-PoN for your project. Try it out on some small data and see what is the difference.
To be sure that I am reading this correctly, are you saying that I should use variant recalibration on my first pass vcf files from Mutect2 and use the outputs of that to create my PoN for a non-model organism? Or can the CreateSomaticPanelofNormals tool calculate artifactual and germline variants on its own, where I could use the first pass vcf files from Mutect2 to directly create my PoN?
Also, what do you mean by "In the tutorial PoN, I do a hand-wavy approximation of masking germline sites in the PoN."
sergey_ko13 Member ✭
Is there any argument against using vcf from first step as -L for the third step for the same sample?
Thank You!
GATK's variant recalibration workflows are meant for germline callsets, e.g. those made with HaplotypeCaller. You should not run your Mutect2 results through these as the annotations in the callsets differ and those that germline recalibration relies on are absent in Mutect2 calls generated with the recommended default arguments.
CreateSomaticPanelOfNormals is a straightforward tool that simply retains sites where variants are called in two or more samples.
For the off-label tutorial, I remove sites in the PoN that are confidently called in sample A and sample B by GenotypeGVCFs. Remember that GenotypeGVCFs calls variants on per-sample GVCFs produced by HaplotypeCaller's
-ERC GVCFmode. Then, for the masking, I use this callset plus a five base mask extension to create the
pon_maskAB.vcfmasked-PoN. I say this is a hand-wavy approximation because (i) I relied on the cutoffs in HaplotypeCaller/GenotypeGVCF to determine passing sites without any fancy population-based filtering like VQSR nor hard-filtering, and (ii) I arbitrarily selected a five base mask without any additional sanity checks or validation to tune appropriateness. I made the motions of masking sites without really checking to see the effects of the approach on sensitivity. To obtain the most sensitive results, albeit with many artifactual calls, omit the PoN altogether.
One thing I wanted to let you know is that our developers have decided to allow Mutect2 to emit germline calls for the normal sample. Code changes are at https://github.com/broadinstitute/gatk/pull/4522, and so these changes will show up in a near-future release of GATK4.
-Loptions should be used cautiously with any of our assembly-based callers, including Mutect2. You need to be sure to provide the caller sufficient padding around the sites of interest, e.g. with the
-ipoption. I do not recommend using small intervals like those from variant calls alone. For consistent and reproducible calling, it's best to allow the tool to traverse the entirety of contigs.
Thank you! I am greatly appreciative of the level of help you have provided on this topic!
I am going to give PoN a try and compare it to calls without PoN. You mention in a previous comment that hard filtering or VQSR can be used. I have a set of calls from HaplotypeCaller, not run on genotype mode and filtered them based upon the recommendations of this article. Is that acceptable or is genotype mode required? I just want to make sure that I am distinguishing between required actions and suggested options.
I have one other question. You mentioned using CombineVariants for the --germline-resource file but CombineVariants is no longer available as a tool in GATK4. Would CatVariants be more appropriate or are there any necessary flags that should be used for Mutect2 to appropriately read the --germline-resource file. I have some loci indicate "set=intersection" or "set=variant" in the info field after using CombineVariants from an older version of gatk and wanted to ensure that this is not problematic for downstream analyses. For example, should I use...
-genotypeMergeOptions UNIQUIFY
--variant:foo input1.vcf \
--variant:bar input2.vcf \
-genotypeMergeOptions PRIORITIZE \
-priority foo,barPost edited by JmeAlena on
Hi @JmeAlena,
I meant to mention Mutect2 has the
--genotype-pon-sitesto include variant sites that are coincident with those in the PoN in the callset, even if they will eventually be filtered.
Can you clarify what you mean by genotype mode? Do you mean the
-ERC GVCFmode? I make no suggestions nor list any requirements. Remember that this workflow that I've proposed is an off-label workflow for you to use at your own risk. It is not an officially supported workflow.
At this point, I think we should involve others in the discussion. I think @davidben would love to hear about your research aims and how this workflow helps you towards them.
It is in the process of being carried over to GATK4. Until this port is complete, you can use CombineVariants from GATK3. I recommend using that from v3.7. You should decide whether additional annotations are useful to you. It is possible to omit the
setannotations by setting
--setKey null. Finally, the tool does not require you set any
--genotypemergeoption. If and how you set this is up to you and depends on what you are combining and how you want variants prioritized.
Ok great! So far everything is working well, thanks to your advice. If I run into downstream issues, I will let you know.
Great to hear @JmeAlena.
Hi @shlee
I had some concerns about my outputs this off-label workflow. We have talked about my experiment a little in previous comments and threads. This may be more appropriate for other threads but I figured I would start here since I used this workflow to generate results.
Mutect2 is calling low frequency variants for me, which is fantastic! However, I re-ran mutect2 with -bamout to visualize my mutations in IGV and how they compare to other samples. My concern is that a mutation will be listed in one sample but not others but I can see in the bam that they do actually exist in the other bam files. It is important to my research to have confidence that it can distinguish novel mutations.
How concerning is this? Is this related to the calculation of uninformative reads discussed in this article? Is there a way around this or what do you recommend?
Remember @JmeAlena, that the bamout also contains artificial haplotypes. It's hard to comment on what may be going on without seeing the alignments. Would it be possible for you to post IGV screenshots of what you are concerned about?
So it appears that the mapping of some regions occur in some samples but not others and this may be an effect of dealing with RNAseq. The combined VCF is at the bottom under the individual bamouts from mutect2. Shown in this screenshot the Mutect2 outputs indicate that only three samples have the mutation but as you can see an additional sample also contains that variant (I arbitrarily chose a locus, I can provide more screenshots if needed).
I understand that some may be considered artifactual but with RNAseq could this be attributed to low depth if it is reporting the same alternate allele? With this being said, I cannot guarantee that the variant doesn't exist in other samples and this limits my confidence in the somatic mutations output by Mutect2.
I understand that not all of these questions may not be your expertise but if there is anything I could have done or could do to prevent this or alleviate the concern from this please let me know.
To confirm, the variants shown in the 4 BAM files are in the bamouts? Then, in the final VCF, only 3 out of 4 samples showing variants in the bamouts are called as variant?
Yes that is correct.
At first I thought that maybe these were occurring at lower frequencies than what Mutect2 could detect without considering it artifactual but in many cases they are all occurring at approximately the same depth.
Hi @shlee
This is a very nice post. I am a little bit confused about the pon file here
For the command you use here,
gatk SelectVariants –V pon.vcf -XL AandB_haplotypecaller.vcf –O pon_maskAB.vcf
if this is a two sample compare study, what sample you use to create this "pon.vcf", is it from one of the sample or both?
Also could you please give more explanations on the five base mask extension?
does that mean when you feed the haplotypecaller.vcf to gatk SelectVariants, you extend the haplotypecaller.vcf region to five bases in both direction?
Hi I used my own way provided below to incoprated this step to the whole workflow:
[2] Modify
A.tablein Excel, e.g. using the
CONCATENATEfunction and add the
#in front of
sed "1c $newline" $A.table > $A.new.table
awk 'BEGIN{OFS="\t"}{if($1!~/#/) {$8="TLOD="$6";AF="$8;$6=".";$7="."}{print $0} }' $A.new.table > $A.af.table
[3] Modify the VCF header. Subset out the header then use nano to modify. change (i)
INFOand (ii) use
kto delete unnecessary lines, etc.
cat $A.vcf |grep '##' |sed 's/##FORMAT/##INFO/g'> $A.header
[4] Concatenate header and body.
cat $A.header $A.af.table > $A.af.vcf
[5] Validate file and index vcf file.
gatk ValidateVariants -V Aaf.vcf
gatk --java-options "-Xmx40g -Djava.io.tmpdir=$TempDir" ValidateVariants -V $A.af.vcf
Thank you!
I do some hackery to reformat the data into these files. I'm pretty sure there are better ways so I left these details out.
What I do involves Excel and is as follows. Please do share any better approaches.
[1] Convert VCF data to table format using VariantsToTable.
gatk VariantsToTable \ -V A.vcf \ -F CHROM -F POS -F ID -F REF -F ALT -F TLOD \ -GF GT -GF AF \ -O A.table
[2] Modify
A.tablein Excel, e.g. using the
Don't forget to add the
#in front of
CHROM. Copy-paste column in-column as values, then remove/modify columns to make a VCF format file. Copy-paste contents to a text editor, e.g. that has preferences set to remove trailing white spaces, and save as text file
[3] Modify the VCF header.
Subset out the header then use nano to modify.
cat A.vcf | grep '##' > A.header nano A.header
Manually change (i)
INFOand (ii) use
kto delete unnecessary lines, etc.
[4] Concatenate header and body.
cat A.header Aaf.table > Aaf.vcf
[5] Validate file.
gatk ValidateVariants -V Aaf.vcf
if this is a two sample compare study, what sample you use to create this "pon.vcf", is it from one of the sample or both?
Have a look at this article.
I will ask Soo Hee to get back to you about your other question.
Any updates about my question above?
Hi @JmeAlena,
Thanks for your patience. Here are my thoughts.
First, in combining your M2 callsets, did you perchance remove filtered calls? It would be good to know whether M2 called a variant for your S6 sample that was subsequently filtered.
Second, remember that Mutect2/FilterMutectCalls parameters are tuned for DNA-Seq, not RNA-Seq, and also are meant to be stringent. So perhaps you should consider tuning the parameters to better suit your RNA data type. There are three stages to consider: (i) upfront read filtering, (ii) assembly machinery and (iii) hard-filtering based on annotation values. I noticed from your screenshot that the coverage for S6 is much lower (30 or 50, hard to tell with resolution) than S7-S9 samples (each >100). However, depth isn't the only factor in calling confident variants. The thing to do is find out at what stage your S6 sample variant is missed, figure out why it was missed (IGV will help here) and see if tuning parameters allows for it to be called, e.g. try
--disable-tool-default-read-filters, and decide if the new setting is appropriate for your entire analysis, etc.
Third, in studying BAMOUTS, folks typically compare it side-by-side to the RAW BAM, i.e. the BAM without reassembly.
Hi @pearlpearl,
Thank you for contributing sed and awk commands. These are great.
I just used the forty-sample PoN from the Mutect2 tutorial. It is important to account for sequencing artifacts, which PoNs do very well even if limited in cohort size.
As for the five-base mask extension, looking back on my notes, I see that I use
--mask-extension 5with GATK's VariantFiltration tool. The command looks something like the following:
gatk VariantFiltration \ -V m2pon.vcf.gz \ --mask hc_tn_genotypegvcfs.vcf.gz \ --mask-extension 5 \ --mask-name hcc1143_hctngenotypegvcf \ -O m2pon_mask_hcc1143_hctngenotypegvcf.vcf.gz
You are asking why I use this extension. In this step, I want to (i) remove common germline variant sites that are variant in samples A and B, so that the workflow can call on them, and (ii) retain all other sites in the PoN that represent artifacts and possible contamination. To quote myself in an answer to @JmeAlena,
I arbitrarily selected a five base mask without any additional sanity checks or validation to tune appropriateness.
Remember that my role with the GATK is to communicate tool features and workflows. The Communications team is not involved in actual research endeavors nor validations of tools nor validations of recommended workflow parameters. This particular workflow is something I developed in a limited time, to show that Mutect2 could be used in a different way than showcased in the official workflow. I hope that researchers will do their own due-diligence towards the parameters they will use.
I use the extension to illustrate that for the sites of interest that are masked, any slight variations in variant call representation are not a factor towards retaining sites in the PoN. To be clear, GATK callers by design left-align variants but this cannot be said to be true for all callers or database resources out there that folks may decide to use as the source of the sites they wish to mask. Also, regions of low-complexity and repeats can be represented differently, based on the read data, even despite left-alignment. So additionally masking areas around AB calls seemed prudent at the time.
Thank you @shlee
In the past I have compared filtered and unfiltered vcfs to indicate whether it was missed or filtered. I will attempt that again and get back to you. I have followed the best practices for RNAseq but essentially replaced haplotype caller with this workflow.
As for the bamouts, I excluded raw bams for visual simplicity but in some cases the regions between the raw and bamout are drastically different. Is this common?
What do you mean by "drastically different"? It is possible in messy regions for the reads to be realigned and the soft clips are gone in the bamout (because an indel has been uncovered), or the region is cleaned up in general. Also, it is possible some reads are filtered out and not output in the bamout.
EADG KielMember ✭✭✭
Hi @shlee, @Sheila and the other people who may still interested in that topic,
I wrote a little not so shiny java-application to create the two site-only-af.vcf, which you need for that workflow. For all the people who don't want to use excel or the sed/awk solution from @pearlpearl .
In addition, I create an example wdl-file+dockerImage so you can easily use it on firecloud if you want.
Just take a look at https://github.com/Selonka/premusa/
Wow, @EADG. Thanks for sharing.
liuxq Member
@shlee , great article. I am still confused about the LOH found by this off-label use. For a specific site, if reference allele is A, normal sample has heterozygous mutation, AB, and tumor sample lost the A allele with only mutant allele B left. Can such kind of LOH be detected by this workflow? thanks.
It seems like there are plans to implement this in the future. Keep an eye on this ticket for updates.
husee Member
I was a liittle confused about the command gatk SelectVariants –V pon.vcf -XL AandB_haplotypecaller.vcf –O pon_maskAB.vcf ,the -XL needs a intervals not a vcf file. In the comment, I found the VariantFiltration , are they the same ?
@husee -L and -XL can both take either an intervals file or a VCF file. If you use a VCF file the program will use the variant positions as interval locations.
Hi, thanks for the wonderful article. I wonder whether you have a similar piece for calling the differences (SNPs, Indels) between two samples using RNA-seq? Say I have one cancer cell line and expose it to a drug and RNA seq both the original and after treatment (triplicate samples for each). Would that be wise if I use the recommedation from https://gatkforums.broadinstitute.org/gatk/discussion/3891/calling-variants-in-rnaseq for data clean up and use the work flow in this article? Thank you.
For somatic variant detection, you should follow the workflow described here. The Best Practice doc for RNA-seq you pointed to is for germline variant calling.
Hi Sheila,
Thanks for the reply. Yes I do understand that the Best Practice doc for RNA-seq is for germline variant calling. However, should I use the data cleaning process (2-pass Star alignment, mark duplicate, sort, split"N"trim, Indel Ralignment and base recalibration) described in that article for RNA-seq data, before using the workflow here for calling "somatic" variants.
Yes you should, with the caveat that some people like to include a somatic variation database (eg COSMIC) in the BQSR step when looking for somatic variants. We have not done a systematic analysis of the benefits of that practice but the reasoning is sound.
Thanks Geraldine. Very helpful input as usual.
mine Member
I have RNA-seq breast cancer data. UnfortunateIy, I have not matched samples. But I have some normal samples that are taken from cancerous people. So I have created my PON file by using these samples.
When I give zero to parameters --af-of-alleles-not-in-resource and --max-population-af as mentioned in here, it will give less "PASS" variations than the results obtained by default values of these parameters.
Which one should I use? I am a little bit confused? Should I give zero or use default values of these parameters?
If you can answer and help, I will be very pleased. Thank you.
kittisakmeaw Member ❠
I have more news than this. But thanks for bringing it to me.:mm
dario_romagnoli Member ✭
Hello @shlee, can you also explain how was


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Okay, it is official...I am now loving watching Russell! Talk about a 180 turn, OMG!!
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text:
Did you hear…
about Charlie and his world record breaking woof? He hails from Adelaide and he can bark 42 times louder than you can talk. His owner Mr Bailey, took him to the Purina Bark in the Park, like a big Day Out for dogs, and Charlie blitzed the competition. Now he's Australia's first ever title holder – well done to the champ!
Didya know?
The world's smallest book, the size of your little finger's finger nail, has names and pictures of flowers. It can't be read without a magnifying glass!
Koala and human fingerprints are almost the same.
The human heart creates enough pressure when it pumps out to the body to squirt blood 30 feet.
It's possible to lead a cow upstairs...but not downstairs.
Q: What gets wetter the more it dries?
A: A towel.
Q: What did Bacon say to Tomato?
A: Lettuce get together!
Q: Where do bees go to the bathroom?
A: At the BP station!


text:
Damage Calculation
|This article or section requires a cleanup in order to meet the Azurilland Wiki's quality standards.
Please edit this page to improve it.
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Damage calculation is the calculation used to determine the damage done by a Pokémon. Only Experts should manually calculate the formula, but it would help you estimate move damage.
Calculation[edit | edit source]
Calculate the values:
A=(2 x Level + 10)/250
Where Level would be Attacking Pokémon's level.
Where Attack is Attack or Special ATK of Atking Pokémon
And Defense is Defense or Special DEF of DEFing Pokémon.
C=Base Power of Move
MOD= STAB x Type x Critical x Others x Rand Value 0.85-1.00
STAB is 1.5x if move is same type as user and 1x if other type
Type is Type Effectiveness= 2x for Super Effective, 0.5x for Not So Effective and 0x for No Effect
Critical is Critical hit= Critical Hit x2 Normal x1
Others is Other Conditions. Input them manually
Rand is Random Value. Minimum damage calculation is 0.85x Maximum Damage is 1x. Remember it is Random
Calculate the formula below based on Values above.
(A x B x C) + 2 x MOD
Imagine if a Turtwig at Lvl 100 had Sp Atk 200, Sp Def 200 and HP 400
It uses Leaf Storm(140 Base) against Piplup at Lvl 90 SP Atk 194,Sp Def 190 and HP 380
Formula is
A=2 x 100/250 = 0.8
B=200/190 =1.052(Rounded up)
MOD = 1.5 x 2x 2x(critical)1x 0.85(Minimum Damage)=5.1
0.8 x1.052 x140 x5.1=600.90=601
Which would be enough to wipe out Piplup.
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text:
Hi there,
I've just bought a pair JBL 4315, quite surprised that this model is quite rare in any forum and web.
I'm cerently using a tube intergrated amp Nelson Audio Image 66i (KT66) with 40W power and feel that the sound is transperant, detailed, accurate...but to my ear, not sweet and warm enough.
I'm planning to change the amp to a single-end 300B amp 15W or less, but not sure if with such low power can drive well the 4315.
Document said sensitivity of 4315 is 89db only, though I feel this monitor would be more 90db.
Any one out there have experience with 4315 pls help to advise.
Your suggestion on amp matching is very appreciated.
Thank you.


text:
First of all, take a look at this tangentially related article from LiveScience a couple of days ago -
The social networking site of choice is related to a student's race, ethnicity and parents' education, a new survey indicates.
The finding "suggests there's less intermingling of users from varying backgrounds on these sites than previously believed," said study leader Eszter Hargittai of the Institute for Policy Research at Northwestern University in Illinois.
Hargittai surveyed more than 1,000 freshmen from the University of Illinois, Chicago.Results show:
Caucasian students prefer Facebook.Hispanic students prefer MySpace.Asian and Asian-American students were more likely than others to "socialize" on Xanga and Friendster. They also used Facebook.Asian and Asian-American students are least likely to use MySpace.
(Remainder of Article)
There's no surprise from this study that people tend to aggregate among similar others in lifestyle and philosophy. So this intersects with thinking about my blog, and what I would hope to accomplish with it (besides the obvious - that writing out my thoughts helps me develop my own thinking, is relaxing and is an excellent way of relieving some of the quickly accumulating societal angst).
Would I love to convince even a few theists to second-guess their view of the universe and start living a life based on reason? Of course I would. Is it a realistic goal for my blog? Absolutely not. We've all seen dozens of blogs that seem dedicated to dissuading readers from a belief in the supernatural. I may add a grain of medicine to the glass of skepticism that some theist has been sipping at anyway and might then be a more potent drink that helps him towards recovery. But it's going to be extremely rare and unlikely - because that type of reader spends very little time at blogs like ours. I still keep such people in mind while writing, because you never know when they may happen by, and my tone and information can either assist or detract from someones journey to the land of reason.
That said, it seems like there's something else I can focus on that really can help a certain group of people. These people are the ones who are most likely to seek out my blog (based on certain key-word searches they might do, or clicking on my link from a similar blog). These people could be called "the choir" as in "Your just preaching to the choir, John. What's the point"? Here, my friends, is the point:
The Exterminator commented on my blog and his, directed at The Chaplain, Ute, JP and others who fit the bill:
"It's nice to have you folks openly joining the dialogue. I don't know whom you're gonna thank this Thanksgiving, although I have a pretty good idea of whom you're not gonna thank. But I'd like to thank you for helping me realize that our little blogs might actually do some good."
Right On! Say it, Brother! There are several of us in this loose knit group of atheists who have been non-believers for years and basically live our lives completely out in the open. While we encourage others to be able to have the freedom we do, we realize the extremely convoluted life situations that others find themselves in and that not everyone can do what we have done - at least not immediately. We don't snub them - we embrace them as brothers and sisters. We have an opportunity to provide them with a community that they may have no where else in their lives. Be it 2 hours a day or 20 minutes a week, they know a place they can go where others think like they do. The folks there are friendly and caring. The members are happy to give personal insights to situations they had 20 or 30 years ago that may apply to something the visitor has been going through this week.
I think I already do this. I think a lot of us do. But I believe we can focus on it a bit more and actively search for these brothers and sisters. You can read it in their blogs if you just take the few minutes to go to a couple new blogs every day and read what's on their minds. Why not invite them to join us. There's no exclusivity at this party.
We already have the community. The Exterminator and Spanish Inquisitor, in particular, have created an extremely friendly environment for meeting and discussing issues related to reason, common-sense, skepticism, rationality, agnosticism and atheism. Additionally, the Exterminator came up with a great project that can be a tool for uniting free-thinkers in a common activity - The Non-Believing Literati. If you haven't joined, maybe you should think about it. There's no great expectations (the book or the pressure). You needn't participate on every book. You are free to pick and choose. And I know Spanish Inquisitor is a bright enough atheist to come up with some other tool for creating a stronger community - especially since he can relate to newer free-thinkers better them some of us other "old timers".
So I'm just throwing this out into our arena of thought to see if others want to make this particular focus more intrinsic to what we are doing by blogging. I'm sure I'll make more of an effort in this area and hope many of you will join me.
Thursday, November 22, 2007
Atheosphere - What's the Use?
First of all, take a look at this tangentially related article from LiveScience a couple of days ago -
posted - 2:41 AM
38 comments:
- Unknown said...
I write on my blog because I enjoy writing, and I have to admit, I enjoy the discussion.
But what you say sounds good. I'm in.
- John Evo said...
I'm not really suggesting that anyone does anything... that you aren't doing already. That's why I like you guys and gals! Maybe just invite people around more.
Happy Thanksgiving, O'Girl. And anyone else who stops by here today.
- The Exterminator said...
Like OG, I write, to a great extent, for my own enjoyment. But I've come more and more to look forward to the discussions, both at my own place and at some of the other great blogs I frequent. It's not only the few that are recent de-cons who need validation and support. I think we all do, at least from time to time.
That's why I urge everyone in the Atheosphere to include a clickable link to his or her personal email. Yeah, you're gonna get some annoying spam you'll wanna ditch. But, on the other hand, you'll also get to exchange meaningful notes, and maybe just general pats on the back that don't always find their way into a comments thread.
I've used emails within the Atheosphere to get or give encouragement, to make suggestions, to seek technical advice, to direct a friend to something he or she might want to read or watch, and just to shoot the shit. A guy whom I now consider one of my best friends in blogworld contacted me by email when he first started blogging just to let me know that he'd appreciate some feedback. I've written to people privately urging them to correct obvious errors that could weaken an otherwise great post; one blogger I like a lot had once mistyped "Tom for "John" in a an otherwise excellent rant about McCain. I've exchanged non-atheist-related emails with another blogger about the use of puzzles in math education; although we both found the subject interesting, it would have been a very dull comment thread. And, of course, as I noted in one of my recent posts, I got an urgent e-note from a recent de-con who hoped I wouldn't "out" her inadvertently.
So get those "Contact Me" links up there, people.
- John Evo said...
That's why I urge everyone in the Atheosphere to include a clickable link to his or her personal email. Yeah, you're gonna get some annoying spam
Great point, Exterminator. I will honestly tell everyone that I've never received any spam or annoying emails from having my email address listed. Now, admittedly, that could be because my blog doesn't draw all that much traffic.
I've enjoyed private emails with a few people in our community and even if I DID get some spam, it would be worth it.
- PhillyChief said...
One big happy godless family. Group hug. :)
- The Exterminator said...
I don't know about the group hug -- or the smiley faces. I'll tell you this, though: The minute somebody starts singing "Kumbaya," I'm outta there.
- DaVinci said...
I started blogging on xanga 4 years ago. Some of the rationalists that I came across really blew my mind. It was my first venture out of my own private agnosticism. I knew others of my ilk in person, but personal communication can be easy compared to blogging. The atheist folks I know in person are (as rationalists) fascinating, so we have loads to talk about besides what we do here in blogs. Blogs tend to be perceived as one-sided because we judge them by standards that we use with folks who we know in person. I say folks not because I'm a hick, I say it because I'm too fucking lazy to type people, sorry. I'm sure all of you are fascinating too in person, and we'd probably talk about all kinds of things besides what we do in our blogs.
The group of people I've met here, I wont name them all, are the best I've found anywhere.
I might check out the book club, but my reading list will probably require that I have a nightlight installed in my coffin at this point. If you have any of the books on my reading list, I might participate though.
- Ute said...
I started my blog under a different name last year, wrote about this and that and never really got into it. Couldn't really identify with my readers either... or the other way around. Then I took a long break, and now I'm back to write about the things that really are on my mind... and to be a part of a community of like minded people from all over the country/world.
So this year I'm thankful for the internet. :)
- PhillyChief said...
When I was in college I was asked to create a comic strip for a new alternative newspaper. I struggled to create characters and plots and it went nowhere. Then the editors had a juicy news tip but couldn't validate the source (ah, the old days when you had to have some sort of credible source before reporting something as news) so they asked me to make a cartoon of the story, depicting the real people involved. No names changed to protect the guilty. Well needless to say, it was a hit and from that moment on I did that every week. No shortage of laughable shit in reality.
Anyway, my point is you need to write about what you know and what deeply matters to you. I think it's the genuineness of the the writing that results from such subject matter that people respond to.
- Ute said...
So true. Now if only that left more time for the book I'm writing.
When I started my blog last year I geared it to my fundamentalist relatives. I tried to tread softly, but I ended up offending them anyways and they all refused to read it. Almost by default I began writing for atheists, educating them about my experiences with the fundamentalist mindset.
I doubt I'll ever convince a hard-core theist, but I have gotten several e-mails from people who were questioning their faith and said I helped them in their journey.
- PhillyChief said...
We can never know just how far reaching the affects of even our mundane actions can be. What we say, what we do, what we write and how we do all of that touches the world. Sometimes we're lucky to hear from people who claim they have been affected by us but I feel that there are countless others out there. There's simply no way to know. The only thing we can know for sure is if we did, said or wrote nothing, we'd certainly have no positive affect on the world but we could very well have a negative one. As comments from recent decons attest to, the more examples and more public outings there are the better it is for them. Those of us never having been in that state of mind or trapped in a fundie world surrounded by nothing but believers have no idea what it must be like. I think every voice on the wind they can catch that says what we say here online encourages them that they aren't alone and they're certainly not crazy or evil as those around them tell them they are.
That's a good point phillychief. When I was in the process of deconversion I felt very alone. My wife kept saying, "but if what you say is true (about the bible), then why has nobody ever noticed before". It was like in two thousand years of church history I was the first person to notice the bible had a few contradictions.
I had no idea that there were others like me and I seriously wondered if I was going insane because nobody else seemed capable of seeing what I was seeing.
The thing that really helped me was finding the Internet Infidels discussion board. I don't really go there much anymore (too busy blogging), but it really helped me to realize I wasn't alone.
- PhillyChief said...
Try Paine's Common Sense. There's someone noticing a few things in the bible may be awry. Let's see, that was over 200 years ago.
Thanks, actually I read it when I was at one of my lowest times during my deconversion and it was like having a light suddenly being turned on in a dark room.
The hard-core theists must pretty much be written off, but there are far more others who are not hard-core. This survey by the Barna Group finds the US adult population to consist of 58 million "active-faith Christians", 20 million atheists and agnostics, and in between, 130 million "American adults who describe themselves as Christians, but who are Christian in name only". Many of the latter are clinging weakly to the tattered remnants of a religion which they hardly really believe in any more, but which they have never heard seriously or intelligently challenged. These people are reachable. They are unlikely to take the initiative to go out and buy Richard Dawkins, but if they run across something on the internet that makes them think about the issue in ways they haven't before, well, who knows?
- The Exterminator said...
infidel, you said: Many of the [130 million Americans who define themselves as Christians but are not regular church-goers] are clinging weakly to the tattered remnants of a religion which they hardly really believe in any more, but which they have never heard seriously or intelligently challenged.
If they've never heard their religion seriously or intelligently challenged, where the fuck have they been lately? There are atheistic spokespeople being interviewed on TV and on the radio. There are dozens of skeptical books available in the chain bookstores. There are newspaper and magazine articles about the "new" atheism. There's an entire Atheosphere engaging in dialogue every single day. Quite a few atheist bloggers, Philly included, seek out fundies to debate. And there are even some moderate Christian bloggers who speak of atheism with tolerance and write about it. So you have to be brain-dead not to have heard that there are a few people out here in the world challenging religion.
You go on to say about the 130 million: These people are reachable.
I'm dubious. Those people are not seeking answers, as most de-converts begin by doing. No, they remain Christians because it's easy to do so; they don't have to think. I see no indication that they'd like to start.
Infidel753 said that hard-core, "active-faith" Christians should be considered pretty much unreachable. It wasn't so long ago that I fell into that demographic. Are they harder to reach? No question about it. But, if you can push the right buttons, which will vary for each individual, you can get them asking some questions. If you can keep them asking questions and encouraging them not to shut down that process, they can come around.
Be prepared to help them through some struggles as they reach the final stages of their de-conversion process. It's easy to let go of little bits of god-belief at a time. It's tough to take that final step and let go of all of it. A blog that I found invaluable in my de-conversion was http://de-conversion.com. It's a place where de-converts share their struggles and encourage each other. It's a nice little community that fills an important niche.
- John Evo said...
Ex, you sound overly pessimistic to me tonight and, as you know, I'm a bit negative myself when it comes to changing people. Then again, I might just be reading that in to what you wrote.
Even if Infidel's numbers are too optimistic, it seems likely to me that there are millions of people out there who could potentially change their positions on religion. Let's look at the 130 million number he tossed out there. I fully agree with you that the vast majority of those are not on a "quest for knowledge". But say 5% of them are. That's 6.5 million people. I think we'd both love to have some of those move away from theism towards a rational world-view.
Look how many of our fellow bloggers claim to have become atheists within the last 5 years. I wouldn't attempt to draw any conclusions that there is something out of the ordinary going on. But even if it is completely ordinary for some people to wake up and see the light, then everything we say and do to promote such seems like a valuable endeavor to me.
Philly said: "We can never know just how far reaching the affects of even our mundane actions can be." I think this hits it. We never know. But because we don't see the end result (a decon) doesn't mean we might not have had some tiny impact on that decision.
This really isn't what my post was about. It was about helping those who had already made the decon leap. Like I said, I still have the others in mind also when I write.
- Ute said...
So, how do I join the Non-Believing Literati anyway??
- John Evo said...
Well, it's very, very difficult Ute.
You're in.
Seriously, we just have to make sure The Exterminator knows that you would like to join. On the left sidebar of his blog you will see a list of the members and whose blogs you can visit to read essays on books we've read.
- The Exterminator said...
I have an answer for you and Philly, but it turned out to be such a long comment that I decided to post on this subject later today, linking back here, of course.
Ute: You are now a member of the Nonbelieving Literati.
- John Evo said...
Ex - look forward to it, as always!
- The Exterminator said...
Getting back to the original post, I'd be interested to hear from chappy, JP, or Lifeguard -- or anyone else who went through the de-conversion process -- about how we can facilitate outreach when they need it.
What could we have done differently to make you people feel more welcome? And is there a way that we can follow Evo's suggestion and draw out the reticent folks who'd like to join our discussions but are maybe just a little intimidated? How can we let them know that we want to hear their ideas -- even though we may disagree with them? And, if we do happen to disagree with them, how do we assure them that, unlike on the Christian blogs they may be used to, disagreement is a vital part of the Atheosphere?
- John Evo said...
Ext - I tend to agree with what The Chaplain said over at your blog about not doing anything other than what we already do.
Hell, we're a pretty good-natured group. I don't think there's a snotty attitude among us. I'm not exactly the sensitive, retiring type but I felt extremely comfortable in interacting with you and the others right from the gate. It seems like all of our posts make clear that we don't think we have the ultimate answers - outside of the basics and that there is plenty of room for dissent in all of our discussions. Anyone who lurks for a few days and reads both posts and comments should feel pretty comfortable, based on the type of people we have. It's even a surprisingly good mixture of males and females.
The only thing I would do outside of the regular community interactions we have is what I mentioned in the post - invite people to join us. If you read something interesting on a blog and it's a person who seems like they might benefit from the group, refer them to a post that relates to what you are hearing from them.
Other than that, it's kind of up to the individuals to step up and participate if they think they have something to add to the discussion. Is it my wishful thinking, or has there been an increase in participation already (talking about the last 60 days or so)?
- The Exterminator said...
I agree with you that it's kind of up to the individuals to step up and participate if they think they have something to add to the discussion. But, truth be told, the very act of joining the discussion -- even if it's just to say "I agree with John" -- may be a big, frightening step for some.
I suppose that's a fear they have to conquer themselves. All of us can watch for the chance to draw out a shy person, but we can't actually force all our readers to feel comfortable enough to leave that very first comment.
- PhillyChief said...
I know I bookmark certain postings from people and drop them into posts that I make on other forums.
A strange thing for me is experiencing religious bullshit on non-religious forums. Some of you are aware of my headaches on the Chiefs forum which is a football fan forum. I've also had some legendary battles on computer graphics forums. I've actually been banned before over the issue. Absolutely ridiculous.
I'm sorry to hear about your problems with the non-religious sites. I read about your issue with the Chiefs site on your blog, but I didn't know about the computer one. How did religion ever come up on those sites? If I'm visiting photo blogs or music blogs, I don't suddenly start writing about camping or politics. Sheesh!
- PhillyChief said...
I had a lot of headaches on CG Society. Everything from bible passages in people's signatures to blatant god talk in posts. It's one thing when it comes up in a general section, but in the middle of a discussion over bugs in a new version of an application? WTF?! That forum has an exceptional set of rules which would be awesome if they actually applied them, or at least applied them blindly to everyone. Instead, they opt for quiet over fairness and we all know how well christians can organize to cry foul and raise a stink. After a ridiculous amount of this crap, I signed a post "btw, there is no god. Have a nice day" and that lead to my first banning (due to my excessive charm, I tend to get invited back to places where I get banned generally). What I found amusing was after that first incident, I had some very nasty crank calls and discovered my email address had been passed out to just about every place on the internet involving gay sex and bestiality. Oh those whacky christians. Naturally, as SI pointed out, these people have all those kinds of places bookmarked or simply committed to memory from repeatedly visiting them. I just found it amusing that these so called moral people would do such things and that I was the bad guy. Like I always say, they are firm believers in the ends justify the means.
- Reason's Whore said...
I would think most lurkers are either 1) too busy/rushed to post 2) found someone had already said what they were going to say 3) are still scoping out the group.
Unwelcome? Pish-tosh.
- Reason's Whore said...
Also re: emails, I used to have my address posted. I prefer to keep my lives segregated. I found too much intrusion and some unwelcome advances.
Of course, that could be the fault of my choice in blog theme. ;D
- The Exterminator said...
Why not set up an email account just for your blogging persona? That way, it's still part of your segregated temple life.
- Spanish Inquisitor said...
Of course, that could be the fault of my choice in blog theme.
And those dirty pictures. ;)
But yes, it's so easy to get another account, through Gmail, or Yahoo. I actually have an account through my home service carrier, which is automatically redirected to my main email account at work, so everything comes to one box. Works nice, and insulates me at the same time.
Sorry for coming to this so late, but being away last week has me playing catch up, both blogging wise and professionally.
OK. I've read this thread, now on to No More Hornets.
We also need to keep in mind that we may rarely have the satisfaction of seeing our efforts, if such they be, bear fruit in any specific way. Looking back at cases where I ended up changing a strongly-held view of my own, it was never because of a single "eureka moment" due to reading some one especially-brilliant polemic. It was always a gradual process driven by an accumulation of exposure to new facts and new ways of looking at them. Many postings on atheist blogs may serve to help along such a process in readers who will eventually abandon what remains of their religion. The point where you come right out and admit to yourself "I don't believe that anymore" is the last step, almost the epilogue, not the beginning -- and certainly not the whole thing.
- John Evo said...
Infidel -
You sound like me! This is exactly the argument I make whenever the "you can't change anyone" challenge comes up.
It depends on how you define "change". If you mean a sudden epiphany that you were able to induce - no, you can't (or maybe you can, but it's probably a one in million thing). If you mean to pull one tiny chink off a coat of armor - yes, you can. You might be 25 years down the road, not know the person anymore, and have no idea how their life has gone, when the final chink falls.
Is it worth spending your time on people who will show no signs of change or gratitude? Only if it's worth it to stop and give directions to a total stranger to a place you are fully familiar with and he is lost. How many times have most of us done that in our lives? Would we do it any other way?
I'm certainly glad that others took the time to write the books and articles that helped me in the past.
- The Exterminator said...
Looking back at cases where I ended up changing a strongly-held view of my own, it was never because of a single "eureka moment" due to reading some one especially-brilliant polemic. It was always a gradual process driven by an accumulation of exposure to new facts and new ways of looking at them.
I agree completely. And I'd also add that what you wrote doesn't apply only to religion. I think it's true of political views and artistic tastes, too.
I think it's true of political views and artistic tastes, too.
Certainly so. Actually it was politics I mostly had in mind when I wrote that. Having grown up in an atheist family, I never had to go through a "deconversion" where religion is concerned.


text:
A web server for hosting Java or servlet applications.
I get the following exception when trying to start SSL on Tomcat5
SEVERE: Exception trying to load keystore /usr/share/tomcat5/.keystore
java.security.KeyStoreException: JKS
at java.security.KeyStore.getInstance(libgcj.so.7rh)
SEVERE: Error starting endpoint
java.io.IOException: Exception trying to load keystore /usr/share/tomcat5/.keystore: JKS
SEVERE: Catalina.start:
LifecycleException: service.getName(): "Catalina"; Protocol handler start failed: java.io.IOException: Exception trying to load keystore /usr/share/tomcat5/.keystore: JKS
- Use keytool to generate a SSL certificate at /usr/share/tomcat5/.keystore. more information
- Switch JVMs from the GNU JVM to the real Sun JVM. source, how to
- Edit /etc/tomcat5/tomcat5.conf to point to the new JVM:
# you could also override JAVA_HOME here
# Where your java installation lives
# JAVA_HOME="/usr/lib/jvm/java"
Setting the Tomcat Proxy
If you have a web application that needs to go through a Proxy but hasn't been set manually in the code, you can add it to Java's startup command line switches:
- Open the Tomcat service manager in the toolbar, and select Configure…
- Select the Java tab
- Add the following lines to your Java Options:


text:
Liberty News
Employees recognized for years of service
Liberty University honored 278 employees at its Years of Service Luncheon on Tuesday, July 10, in the club pavilion level of Williams Stadium tower.
This is the second year for the event that honors employees who have hit milestones with the university and its related ministries, having served five, 10, 15, 20, 25, 30, and 35 years. To view the names of the employees and years of service, click here.
This year four retirees were also honored: Mr. Robert N. Mateer, Professor of Business (28 years); Dr. Sandra V. Rumore, Professor of Mathematics (28 years); Mrs. Eileen Wagner, Office Manager for Victory FM (27 years); and Mr. Robert C. Rencher, Jr., Associate Professor of Business (21 years).
The event is part of Liberty's You Matter campaign, a new, university-wide initiative to provide faculty and staff with the resources needed to carry out the university's mission to be used by God to change students' lives.
"Years of service matter at Liberty University and seniority matters," Dr. Ron Godwin, Liberty's Senior Vice President for Academic Affairs/Provost, told employees at the luncheon. "People who've invested, sacrificed, dedicated large sections of their adult life to the students of this university matter. They don't just matter to the senior leadership here at Liberty; I believe firmly with all my heart they matter to God. I believe that what you've done, He knows about it, He recognizes, He appreciates it and that's the most important recognition that any of us can enjoy."
Chancellor Jerry Falwell, Jr. asked all to stand, by their years of service, and presented the plaques to the retirees. Employees' pictures were taken with Falwell and his wife, Becki, following the luncheon.
"We are blessed at Liberty with the best faculty and staff in the world," Falwell said. "I knew that when I was here (as a student), and I hear that all the time from our students ... they are not just here to make a living, they really take a personal interest in all the students and the students go out of their way to tell us that."


text:
If Hewlett-Packard introduces an Android tablet, the newfound rivalry with Microsoft will be one motivating factor, according to analysts.
"I can see why they would go down this route instead of sticking with Microsoft for everything," said Ben Bajarin, a principal at Creative Strategies.
That may be putting it charitably. "[PC makers] are pissed off at Microsoft. That's the general mood," said Roger Kay, principal analyst at Endpoint Technologies, referring to Microsoft's entry into the PC/tablet market with Surface.
Surface practically precluded HP from coming out with a Windows RT tablet based on an ARM chip -- the same silicon used for Android devices -- Kay said.
In fact, HP scuttled plans last year to bring out an RT tablet and then dissed Microsoft's device publicly, calling it "slow...kludgy" and "expensive."
But that of course isn't the only reason HP would do an Android tablet. It could, for instance, try to take the lead in bringing Android tablets to large corporate customers, Bajarin said.
To some extent, Samsung is doing that in phones now, but HP, being the largest PC maker in the world, could spearhead Android for business, according to Bajarin. "They could see that as a big opportunity," he said.
And being late to the Android market isn't all bad. "All the development in Android up to this point accrues so they can claim to be on board without a whole lot of development that they have to do independently," Kay said.
This would come about two years after HP's WebOS tablet debacle. In August of 2011, the company terminated its TouchPad only a month and a half after the device's introduction.
It also ended plans for a WebOS-based phone at that time.
HP currently offers the Windows 8-based ElitePad 900 tablet and a Windows 8 hybrid tablet-laptop: the Envy x2. Both are based on Intel's power-efficient -- and relatively slow -- Atom processor.
And it already has one product based on a Google operating system. It's selling a Chromebook for $330.
HP declined to comment.


text:
A global online ad scam may result in over 300,000 Internet users losing their access to the web from July 9 this year, said the U.S. Federal Bureau of Investigations (F.B.I.) on Wednesday, after shutting down an Estonian hacking ring that has been in operation for at least four years.
The virus, named "DNS Changer", had been designed to redirect the web browsers of victims from sites they wanted to visit to ones controlled by the gang. Though the perpetrators have already been caught and their servers substituted by clean ones, the F.B.I will need to turn off the replacement servers on July 9, with the cost of the servers having run up to about $87,000 thus far.
"We started to realize that we might have a little bit of a problem on our hands because … if we just pulled the plug on their criminal infrastructure and threw everybody in jail, the victims of this were going to be without Internet service," said Tom Grasso, an FBI supervisory special agent, to the Associated Press.
"The average user would open up Internet Explorer and get 'page not found' and think the Internet is broken."
Related: Infographic: Millions Left Behind By The Internet Revolution
Related: Infographic: The Internet - Then vs. Now
Related: Internet Statistics (Internet Users, Internet Hosts, Country TLD)
Accordingly, the F.B.I. has set up a new website for Internet users to check if they have been infected, with further instructions on the site how to fix the problem.
While the F.B.I. are unable to pinpoint the exact number of victims involved, they believe that the sum is likely to be around 360,000 – down from the original estimate of 568,000 users, coming just days after the arrest.
The problem will also not be confined to just the United States, with about 20,000 victims expected to come from Italy, India, England, and Germany each, while a significant number of users from Spain, France, Canada, China and Mexico are also expected to be affected.
The hackers in the case are believed to be have earned over US$14 million ($17.2 million) in the process. Victims are unlikely to be aware of the issue as the virus has no observable outward symptoms apart from a slight decrease in web-browsing speed, coupled with the fact that it is able to circumvent any antivirus software that a computer may have.
Check if your computer is infected via this link.


text:
JACKSONVILLE, Fla. – It was business as usual at the Fraternal Order of Police meeting on Beach Boulevard Tuesday night.
The non-profit voted to elect an acting president and vice president after previous leaders, Nelson Cuba and Robbie Freitas are accused of taking part in a $290 million Internet Cafe illegal gambling operation.
"I want to re-emphasize that the actions and the alleged transgressions of the president and the first vice president in no way is indicative for the men and women who put their life on the line every day for this community," said Channel 4 Crime Analyst and FOP member, Ken Jefferson.
Jefferson told Channel 4 that the FOP voted Tuesday night to elect an interim president and vice president for the non-profit. Jefferson said Steve Amos was elected acting president and Lt. Larry Gayle was elected as acting vice president by the FOP board Tuesday night.
"I left this meeting feeling good, even better actually about the Fraternal Order of Police, even though the two top people have committed their own transgressions, allegedly, the business of the FOP is continually moving forward," said Jefferson.
Another looming question is whether the popular Guns and Hoses Charity event will take place as scheduled. Jefferson said Board members spoke about the event Tuesday night, and that it will go on as planned.
"Guns and hoses, one of the biggest fundraisers for the FOP," said Jefferson. "They were pleased to announced that Guns and Hoses is going forward, it will be held again this year, they are looking for a large number of people to be in attendance as it has been in the past so Guns and Hoses one of the biggest fundraisers, will continue to go forward."


text:
Olympians, world champions to headline Pegula Ice Arena figure skating show
Olympians, world champions to headline Pegula Ice Arena figure skating show
UNIVERSITY PARK, Pa. -- The Pegula Ice Arena will once again host international figure skating champions and Olympians this October as part of the Musselman's Apple Sauce Family Skating Tribute.
Award-winning singer-songwriter Amy Grant will perform live in the family-themed show at 5 p.m. Oct. 19 featuring skating stars and Olympic gold medalists Ekaterina Gordeeva and Ilia Kulik, and two-time Olympic medalist Nancy Kerrigan. Hosted by skating champions (and parents) Kristi Yamaguchi and Michael Weiss, the star-studded cast is scheduled to include numerous World Champions and Olympic medalists.
Click here to view the full press release.
An exclusive pre-sale opportunity is being offered for Penn Staters to access tickets prior to the general public sale, which begins Aug. 29. Click here and enter "STATE" in the offer code to access pre-sale tickets.