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Git & Version Control With Tower or on the Command Line. PDF, ePub, Mobi for all devices; Start Now for Free. 20+ high quality videos one topic per video; highly visual way of learning real life workflows.This tutorial assumes you are using Py. Clone 0. 1. 2. 3. Most of this tutorial will apply to the older 0. This tutorial also assumes you are working in a Unix like environment. I have tested it on Linux, and it should work on Mac though I can't guarantee that. It almost certainly will not work for Windows and there will likely never be support in Py. Clone for Windows. Historically Py. Clone has referred to the proportion of cancer cells which contain a mutation as the cellular frequency of the mutation. Recent publications in the field have referred to the same quantity as the cellular prevlance of the mutation. In this document we will generally use prevalence, but some of the Py. Clone functions use frequency. Py. Clone requires that you generate prior information about the genotype of each mutation in the sample. In principle this depends on the algorithm(s) you use for copy number inference, tumour content prediction and your own beliefs. In practice specifying priors is challenging so Py.
Clone includes some functionality to automatically generate the required prior information based on simpler input information. Before you can use Py. Clone you will need the following information for each mutation in the sample. Allelic count data from a sequencing experiment. Py. Clone requires that you specify the number of reads overlapping the mutation which contain the reference allele and the number of reads which contain the variant allele. The copy number of the genomic region containing the mutation. Py. Clone can work with either predictions of total copy number or parental (allele specific) copy number. In general performance will be better if you can specify parental copy number. In addition to above data for each mutation, Py. Clone can also use an estimate of the tumour content of the sample. The tumour content is not strictly required, but if it is not passed performance will be worse. In addition the estimates of cellular prevalence of the mutations will need to be interpreted differently. If you specify the tumour content, then the cellular prevalence estimates represent the fraction of cancer cells which contain the mutation. If you do not specify the tumour content, which in practice means setting it to 1. This means that the highest estimated cellular prevalence will be less then or equal to the true tumour content. Note : If you have estimates of tumour content use them, otherwise the inferred cellular prevalences may exceed the predicted tumour content. The sequencing data can be obtained from any sequencing platform which provides digital allelic count information. For examples: Hi. Seq, Mi. Seq, 4. 54 and Ion Torrent sequencers would all provided the required data. The data will of course need to be aligned and the allelic counts extracted. In principle whole genomes shotgun sequencing (WGSS) or exome capture sequencing data could be used. In practice the depth of these approaches will be to low for an accurate Py. Clone analysis. The preferred approach is to use deep sequence data acquired by targeted amplicon sequencing or custom capture arrays. The copy number information can be elicited from either arrays such as the Affymetrix SNP6. WGSS data. Computational tools will need to be applied in either case to infer the copy number profiles of the genomes. Tools which can predict parental copy number are ideal, and even better are tools which also provide an estimate of tumour content. Assuming you have derived a copy number profile for your samples, you will need to extract the copy number of the segments which contain your mutations. For this tutorial we will use data from a mixture of normal tissue samples. There are four samples in this dataset which were generated by mixing tissues from four 1. The data was deeply sequenced using the Illumina Mi. Seq platform. Positions in which only one of the cases has a variant genotype (AB or BB) are included in this dataset. Conceptually this is equivalent to a sample with four populations of diploid clones, which share no mutations. Learn how to use Git with Code School’s interactive course, Try Git. Because we excluded sex chromosomes, the total copy number of all positions is 2. For this dataset we still need to get the parental copy number for mutation. This can be done since we have the predicted genotype of the variants (AB or BB). In the case the mutation is AB the major and minor copy numbers would both be 1. In the case the genotype was BB the major copy number would be 2 and the minor copy number would be one. Below is an example of the first two rows of one of the input files, SRR3. The input files are located under the tsv/ folder. The first row is the header, the subsequent rows correspond to mutations. There are 6 mandatory fields in for the input file. In general specifying the gene for the mutation is a bad idea in case a gene contains multiple mutations. Usually some combination of gene name and genomic coordinates is a good choice. In this case I have used the case with the variant, the genotype of mutation in the variant case and the genomic coordinates. In most cases this will be 2, with the following exceptions (there may be some others I haven't considered). If the sample is from a male and the mutation is on a sex chromosomes (X or Y) you would expect the normal cells to have copy number 1. If the normal tissue has a germline copy number variant you would need to set the copy number to the predicted value. The only way to get this is to run a copy number analysis on normal tissue from the same donor. The convention is that the major copy number is the larger of the two values. Note : If you only have total copy number for the tumour, not parental copy number, you can set the minor. When we use the Py. Clone build. By default the command assumes parental copy number information is being passed. This files also contains 3 additional fields. Py. Clone will ignore these fields during analyses, and they are only useful for your own annotations. Any fields beyond the 6 mandatory ones mentioned above will be ignored by Py. Clone. For reference the additional 3 fields in this file arevariant. There is one file and one folder in this directory. Py. Clone analysis. The first thing we will need to do is take the files in tsv/ and convert them to a format Py. Clone can work with. Specifically we need to specify the possible states of each mutation and their prior probabilities. The state of a mutation is combination of genotypes for the normal, reference and variant populations. Py. Clone includes a command build. There are some options for the build. The first few lines of the file yaml/SRR3. NA1. 21. 56: BB: chr. The first linespecifies we are listing out the mutations for this sample. The next line- id: NA1. BB: chr. 2: 1. 75. NA1. 21. 56: BB: chr. Note the - indicates were are starting a new mutation entry. The linesand specify the reference and variant counts for the mutations. The state priors are specified bystates: -. For each state we specify 4 values: g. Recall the reference sub- populations consists of all cancer cells which lack the mutation. Thus valid genotypes here should not contain a B allele. For examples A, AA, AAA, AAAAAAAA are all valid but B, AB, BB, AAAAB are invalid. Recall the variant sub- populations consists of all cancer cells which posses the mutation. Thus valid genotypes should contain at least one B allele. For example B, AB, BB, ABBB are all valid but A, AA, AAB are not valid. The relative prior belief you have in this state versus the others specified. This value will normalised so that the sum over the prior beliefs for all states for a mutation equals 1. Py. Clone won't warn you about invalid entries so you need to be careful if you create the yaml files by hand. This means that you could include germline mutations or LOH events. You can also re- purpose the model for other applications. Before Py. Clone can perform an analysis we need to create one more YAML format file. This file tells Py. Clone The directory structure on the system Where the file with the mutation informations reside. The model which we want to run. The tumour content and error rates for sequencing for each sample were are going to analyse. Various parameter settings for the model. Their is no helper function included with Py. Clone so this file will have to be created manually. The tutorial data includes a file config. The file looks likenum. More iterations will lead to a more accurate estimate of the posterior distribution at the cost of more computational effort. Note: One way to check if you have run a sufficient number of iterations is to perform the analysis twice from different initialisations (default if you don't set the - -seed flag with the analyse command). If the results are the same then it is likely that enough iterations have been run. If not you will need to re- run for more iterations. Note: In my experience 1. Burnin is set during the post- processing phase. The next linesbase. The default values are uniformly spread over . Most users will not need to change these default values. The next few linesconcentration: value: 1. Dirichlet Process (DP). Again most users will not need to edit these and the defaults should suffice. If the linesprior: shape: 1. The first thing we will do is add an entry to specify which density (model) we want to use. There are several options gaussian : This option will use an infinite Gaussian mixture model (IGMM) fit to the variant allelic frequencies. This option will use an infinite Binomial mixture model (IBMM) fit to allelic count data. This will be the choice most users will want. We will use the Py. Clone model with the Beta Binomial emission, to specify this add following line to the config. We will add the following lines to the file to do this. To keep the configuration file more readable Py. Clone specifies a working directory where all analyses will be performed, every other path in the config. To do this add the lineworking. To do this add the following linewhich will cause Py. Clone to place the output in /path/to/tutorial/directory/trace. Next we need to tell Py. Git - Documentation. Pro Git is written by Scott Chacon and Ben Straub and published by Apress. How To Disable Windows 8. Startup Programs. In previous versions of Windows, you can help it start up faster by disabling startup programs with Task manager. You can still do it in Windows 8. Task Manager has been revamped since the days of Windows 7, and disabling startup programs is easier, plus more information about the apps and programs is provided. While Windows 8. x does boot noticeably faster than Windows 7 and earlier, you can make it boot even faster by disabling startup programs. Note: This article has been updated to reflect the changes from Windows 8 to Windows 8. Hi, To autostart a program that does not have that option in its setup just copy the icon to your startup folder. For ALL Users copy to : 'C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Startup' Right Click Start Button - Explorer All Users and navigate to.
Disable Windows 8. Startup Programs. There are, of course, a couple ways to get to the same place with Windows, and that’s no different in Windows 8. First, from the Modern Start screen type: msconfig and hit Enter. Or from the desktop, just like Windows 7, right- click the Taskbar and select Task Manager. Either way you do it, the new Task Manger will open on the desktop. Click the Startup tab to see the items set to run when you boot your system. Right- click on any of the programs to and click Disable. While Windows Vista included a useful interface for managing which applications could run at startup, Microsoft removed it from Windows 7, forcing users to rely on more old-fashioned utilities. But Windows 8 includes an even better solution for this problem. And if you are using a lot of desktop. The program will still appear on the list, but the Status will change to Disabled. Right- click an app again and select Enable to have it run during startup. Notice that when you right- click a program in under the Startup tab, you’ll see more options. This allows you to get a better understanding of what each program is or does before you disable it. I find the option to search for the program online to be particularly beneficial. We’re all guilty of installing desktop programs or apps, using them once, and after a year you have no clue what they are. For more details, check out our guide on new features available in the Windows 8. Startup tab in Task Manager. About Brian Burgess. Based in MN, Brian Burgess is Editor in Chief at groovy. Post. He also has contributed to other notable tech sites including Information. Week and How- To Geek. Follow him on Twitter @mysticgeek. Don't Miss a Single Tip! Ways to Change Startup Programs in Windows 7. WINSpeed 9. 0 - Download - 4shared.
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PDF Download Problems with IIS7.5 on Windows Server 2008 R2. Volvo 8. 50 BTCCThis article is about the Volvo 8. After many years not being active in motorsports it was time to give Volvo a more sporty image. Volvo at the BTCCWhen the Volvo 8. Volvo wanted to upgrade their image. The 8. 50 was a very good step into the right direction but despite the great (more sporty) handling compared with the other Volvos the direction of Volvo felt the sporty character of Volvo should be increased. Volvo left motorsport- activities in 1. Volvo deciced the British Touring Car Championship (BTCC) should be the perfect podium for its racing activities. The Volvo 8. 50 Touring Car prototype of Steffansson Automotive. Volvo Senior Vice President Martin Rybeck approached Steffansson Automotive (SAM) to design a prototype car for racing, based on the 8. Volvo gave a lot of information and support of the 8. SAM. Volvo also promised to gave a bodyshell. But when SAM went to Volvo to pick up the bodyshell only 8. Estates (the facelifted versions, with new headlights and bumpers) were produced. But the project couldn’t have any delay so Volvo and SAM decided to use the Estate bodyshell. When Rybeck heard about the story he thought it would be a great idea to race with an estate! The marketing potential should be huge, but when it becomes a failure it would be embarrassing for Volvo. The car is now for sale at Blocket. The 8. 50 Estate racer prototype of SAM was very promising. To be sure the Estate racing car shouldn’t become a failure Volvo tested the saloon and Estate in a windtunnel. The results were very surprising: the Estate should have a better downforce due its large flat roof. TWR and Volvo. Volvo decided to take the project to the next level and Tom Walkinshaw (of TWR, Tom Walkinshaw Racing) was asked to have a close look on the Estate- version as racing car. The motorsport experts of TWR confirmed that when the weight could be taken to the legal minimum, there shouldn’t be a lot difference between the saloon and the Estate on the circuit. Volvo confirmed joining the BTCC at the end of 1. TWR a three- year contract for building and designing the 8. BTCC racing cars. The Columbia-class submarine, also known as the Ohio Replacement Submarine (formerly the SSBN-X Future Follow-on Submarine) is a future United States Navy nuclear submarine designed to replace the Trident missile-armed Ohio. GAO program report for SSBN-X overall, Cost estimates. April 7/14: Specifications. The US Navy has reportedly finalized the specifications for their new SSBNs. They’ll be about as long as the current Ohio Class, but with 8. Nuclear-Powered Ships (Updated June 2016) Nuclear power is particularly suitable for vessels which need to be at sea for long periods without refuelling, or for powerful submarine propulsion. Over 140 ships are powered by more. 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With all due respect: things like this may have been done before but Vince Briel’s Altair emulator is a real emulator (and by the way it uses the Propeller only as terminal emulator, not as CPU), whereas this. Volvo confirmed it should enter the BTCC championship with a Volvo 8. Estate. The 8. 50 Estate racer was equipped with a 2. The car was a frontwheeldrive (FWD) and has a X- Trac 6- speed sequential gearbox. The brakes were all ventilated discs by Brembo (which also supplied the brake calipers). Stefano Brizzolara is Assistant Director for Research at MIT Sea Grant. The expert naval architect and renowned ship designer was the Visiting Peabody Associate Professor at MIT's Mechanical Engineering Department for 2012.Born to Race Just how close a pair of custom-built racers came to unseating the kings of Reno. Wheels are from OZ (1. Dunlop. A sprint from 0- 1. Volvo confirmed former Formula One driver Jan Lammers (The Netherlands) and Rickard Rydell (Sweden) as their drivers for the 1. The official team name was: Volvo 8. Racing. Former F1 driver Jan Lammers in a March- Ilmor in 1. Volvo 8. 50 Estate in the BTCC 1. The first race of the season was on April 1. TWR had some serious troubles to finish the first cars and time was running out. Just before the first test sessions at Snetterton (April 4 1. Just in time! The livery of the 8. Estate in the BTCCThe 1. Lammers and Rydell) and in the race a fifth place. Volvo ended on a sixth place in the Constructors Championship at the BTCC that season. The car did pretty well in high- speed corners but in slow and sharp corners there was a lack of grip and traction, caused by the weird weight balance of the car. After the season Lammers abandoned the BTCC because he didn’t like the driving- style of touringcars. And later he admitted he didn’t support the Volvo 8. Estate BTCC car for 1. Lammers drove a 8. T- 5 himself back then). Another funny story told in some interviews (like Autoweek, the Dutch version of Autobild) with Lammers is how the other drivers responded to an estate racing car: some drivers called the 8. Estate a baker’s car and being overtaken by the “pizza delivery” was also not done. Lammers said when he or Rydell overtake a car they would be hit at the back some corners later (the 8. BTCC at that time) and some drivers complained about the sight behind the 8. Estate: when you drive behind it you couldn’t see anything due the stationwagon- bodyshape. But there was also good news: the 8. Lammers said: “At that time my handicap dropped down faster than my laptimes!” Lammers flying around in his Volvo 8. Estate. 19. 95: goodbye Volvo Estate racer, welcome 8. BTCCIn 1. 99. 5 the rules of the cars design were changed. Since the 1. 99. 5- season it was allowed to have front- and rear wings but those wings weren’t allowed to pass the rear bumper or be higher than the roofline. These new regulations only allowed Volvo to use a 8. Estate. When Volvo should appear with the Estate (including a rear wing) at the starting grid it could be banned. Rickard Rydell and Tim Harvey with the new 8. Saloon racer. Because the saloon with rear wing had a much better downforce than the Estate without rear spoiler the choice for the 1. Volvo was going to race with the 8. In 1. 99. 5 there were also some other changes (besides the front and rear wings): a catalytic converter was now a mandatory. Because Jan Lammers didn’t want to race another season at the BTCC Tim Harvey (England) took over Lammers’ place at Volvo. The livery and sponsors for the 1. The 1. 99. 5 BTCC season was much better than 1. Volvo: Rydell took several pole positions and won four races! Rydell was a title contender that year but unfortunately didn’t win the title. Harvey also had a good season with 2 wins and several podium finishes. It was a very good season. Tim Harvey left the team and signed at Peugeot, who entered the BTCC with the brand new 4. The young talented driver and Formula 3 champion Kelvin Burt (England) replaced Harvey. Besides the new driver and slightly changed team name there were some other small changes: Michelin was the new supplier of tires and OZ Wheels was replaced by BBS (the size went from 1. The front brakes (discs and calipers) were changed from Brembo to AP. The steering system was changed to a new version made by TWR. Rydell in action at Brands Hatch. That year was slightly better than 1. Rickard Rydell took 5 pole positions and won 4 races, which delivered him a thirth place in the final standings (1. Burt finished 1. 1th in the final standings (6. TWR/Volvo 8. 50 Racing managed to finish third in the Constructors Championship. Racing car. It was replaced by the Volvo S4. S4. 0R) in 1. 99. One of the 8. 50s that was used in the 1. BTCC- season was used in the STCC (Swedish Touring Car Championship) in 1. After that season the car was moved to the Volvo Museum in Sweden. Estate still racing in the DSCToday a Volvo 8. Estate is still in use as a racecar: Dutch driver Jochen Pethke (who was racing in the Volvo 3. Cup at Zandvoort) is now active in the Dutch Supercar Challenge (DSC). The car isn’t exactly the same as it was in the good old days: the 6- speed sequential gearbox of X- Trac is replaced by a regular 5- speed manual transmission. The car has a 2. 3 litre 5- cylinder turbocharged engine. The Volvo 8. 50 of Pethke in action. It’s hard to verify, but the rumours says the remaining Volvo 8. Racing- cars (the cars that didn’t go back to Volvo Sweden) should be destroyed in Switzerland. The reason was very simple: nobody should see which modifications made the car faster (of course something like that is top secret). But for some reason one car survived and was stored in Mijdrecht (The Netherlands) for a long time. The engine was removed. Pethke heard about the 8. Estate racer and wanted to buy the car. After some tough negotiations Pehtke managed to convince the previous owner and bought the car. He fitted a turbocharged engine into the car, made some minor modifications to match the DSC- regulations and is racing with the car these days. Complementary and alternative medicine for the. Complementary and alternative medicine for multiple sclerosis. Central Institute of Mental Health, University of Heidelberg, J 5. PDF File: Complementary And Alternative Medicine And Multiple Sclerosis 2nd Edition - WWRG15-CAAMAMS2EPDF-7 3/4. Related PDFs for Complementary And Alternative. Browse journals by subject. Accept. 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