Download File P_G_1.zip _BEST_
Note: This researcher contribution consists of a SAS file (.sas7bdat), a text file (.txt), and related documentation. The data contain the polygenic index for phenotypes described in Becker et al. (2021), for European-ancestry HRS respondents who provided salivary DNA between 2006 and 2012. Additional methodology is available in the documentation.
Download File P_G_1.zip
Becker, J., Burik, C.A.P., Goldman, G., Wang, N., Jayashankar, H., Bennett, M., Belsky, D.W., Karlsson Linnér, R., Ahlskog, R., Kleinman, A., Hinds, D.A., 23andMe Research Group, Caspi, A., Corcoran, D.L., Moffitt, T.E., Poulton, R., Sugden, K., Williams, B.S., Harris, K.M., Steptoe, A., Ajnakina, O., Milani, L., Esko, T., Iacono, W.G., McGue, T., Magnusson, P.K.E., Mallard, T.T., Harden, K.P., Tucker-Drob, E.M., Herd, P., Freese, J., Young, A., Beauchamp, J.P., Koellinger, P.D., Oskarsson, S., Johannesson, M., Visscher, P.M., Meyer, M.N., Laibson, D., Cesarini, D., Benjamin, D.J., Turley, P., and Okbay, A. (2021). Resource Profile and User Guide of the Polygenic Index Repository. Nature Human Behaviour. Published online June 17. doi:10.1038/s41562-021-01119-3.
Go back to the set up instructions. There are two programs you need to run that create the data sets. Run those two programs. From the files you downloaded the programs are called: setup.sas and createdata.sas
You're not the first who missed that dataset. Maybe it's in the same folder where @OmniDIYer found it? See this recent thread. Otherwise, I'd search for the file np_summary.sas7bdat on the computer where it's supposed to be, using the operating system's search tool. Once you've found it, you should be able to apply a similar LIBNAME statement as I suggested in the other thread.
Click on the relevant zip file to download it to your desktop. You can then choose the logo file format EPS, JPEG or PNG to print the logo in colour or black and white. If you use a printing company, copy and email the relevant zip file link to them:
Select Target Platform Click on the green buttons that describe your target platform. Only supported platforms will be shown. By downloading and using the software, you agree to fully comply with the terms and conditions of the HPC SDK Software...
This version is the complete version of GAMESS (with Tinker, NEO, and VB2000) precompiledfor use on 64-bit Windows. To download any of these Windows binaries, just click on your choice below, enter the username (which is always source), and the current downloadpassword, from the e-mail you should have already received.Once downloaded, you just need to double click on the .msi file, and read the instructions.
If you have problems with your installation, and have made a good faith effort in reading the README or usage instructions of the 'rungms.bat' or 'runall.bat' files, please send an email to ssok1+WindowsUsers@iastate.edu
Now, to finish the CUDA setup, we can do a little system configuration to put cuda/bin on the default path and add a conf file to get cuda/lib64 on the library path. (this may help if you had some of the sample jobs fail ?
After downloading please verify the integrity of your Gpg4win package. Then double-click on the file you have downloaded and follow the instructions on the screen (or look at the documentation) and read the current README file.Gpg4win Compendium 3.0.0(Released: 2016-11-30)You find the current PDF and HTML version of the Gpg4win Compendiumhere:
In the change historyyou will find information about the most relevant changes and whichversion of the products each of the releases contained.Also, you will find direct download link for the old releases.
Step 4. All the agent desktop interaction is registered and sent to the local storage logs. To collect the logs, navigate to :8445/desktop/locallog and copy the content into a text file. Save the file for further analysis.
The most common logs that you need to collect are the Engine. The default level of traces for the CVVB Engine tarces is enough to troubleshoot most issues. However, if you need to change the level of traces for a specific scenario, Cisco recommends that you use the pre-defined System Log Profiles
Step 3. Check the profile that you want to enable for the specific scenario and click the Enable button. For example enable the profile CallControlVVB for SIP related issues or MRCPVVB for issues related to Automatic Speech Recognition and Text to Speech (ASR/TTS) interaction.
If you need to create a new SSH key pair for logging in to AWS EC2, pull down the menu item that says Choose an existing key pair and select Create a new key pair. Give your key pair a name in the following text entry box, then click on the Download Key Pair button. The downloaded file should have a name with a.pem extension, e.g. MyKey.pem. Save this file in a safe location, because you will need it to log in to the AWS EC2 instances you create.
You can now connect and login to your instance. For example, suppose your instance has been brought up on an IP address of 192.168.144.127 and you are using the private key stored in the file MyKey.pem. If you use the OpenSSH client bundled with Linux, macOS, FreeBSD, or various other operating systems, you can issue the following command to log into your instance:
If you see a message such as *** System restart required ***, the underlying Ubuntu Linux operating system has automatically downloaded an important security update and the system needs to be rebooted in order to apply it. You should issue the following command to reboot your instance:
When the build completes, an executable named clover_leaf appears in the CloverLeaf_Serial subdirectory. Try running CloverLeaf using the clover_bm32.in input deck. CloverLeaf expects its input file to be named clover.in. First move the existing clover.in file out of the way and then copy the clover_bm32.in file from the InputDecks subdirectory to the current directory as clover.in:
JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway.
JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at nayaklab/jcoda.
In an effort to simplify the process, PAL2NAL (v12) takes pre-aligned protein and the corresponding unaligned coding DNA to generate codon-delimited alignments. While useful, PAL2NAL is constrained to pairwise dN/dS analysis, does not include graphing, and does not allow the user to edit the codeml control file . The popular program PAML (Phylogenetic Analysis by Maximum Likelihood) is able to perform both pairwise and site-based dN/dS calculations. However, it does not have a GUI (graphical user interface) and visualization of the output data can be cumbersome. In addition, it requires the input of pre-aligned sequences . More recently, IDEA (Interactive Display For Evolutionary Analyses) has implemented a GUI for both PAML and Phylip (Phylogeny Inference Package) and is amenable for high throughput genome-wide analysis . While IDEA is a powerful tool, it does not run on the Windows operating system, requires the separate installation of several support programs, uses multiple languages, generates graphs that are difficult to configure, and also requires a codon-delimited alignment.
JCoDA takes advantage of the codeml executable included in the PAML package to implement site-specific dN/dS calculation. Similar to pairwise comparisons, JCoDA converts all inputted sequences to Phylip format and feeds them to codeml. In order for a site-based dN/dS calculation to be performed, the user must provide a tree file and set its path for use in the GUI. To allow for this operation, the JCoDA package includes a Java based graphical interface for the Phylip package , ). The Phylip Graphical Interface (PGI) allows for the generation of trees using neighbor-joining, parsimony, or maximum likelihood based methods of either DNA or protein. Regardless of the source of the tree file, JCoDA will accept any tree in Phylip format.
JCoDA implements M7 (fit to a beta distribution, dN/dS > 1 disallowed) -vs- M8 (fit to a beta distribution, dN/dS > 1 allowed) and M1a (nearly neutral) -vs- M2a (positive selection) in conjunction with the likelihood ratio test to check for evidence of positive selection . To maintain JCoDA's flexibility, the user is given the option to access the complete codeml control file as a selectable advanced options tab to vary other parameters.
Navigation in JCoDA has been designed around the use of a tabbed GUI that allows for shuffling between graphs and sequence alignments (Figure 2). We have implemented JFreeChart to generate robust graphs of dN/dS scores by both sliding window and site-specific methods. The graphs are extensively customizable, dynamically scaled, and can be saved as PNG (Portable Network Graphics) files (Figure 3 and 4A). The user can export protein and DNA alignment files in ClustalW, Phylip (v3.2 and v4), and hybrid protein/DNA codon-delimited formats using the file menu. The dN/dS scores from all models selected, including p values, can be exported as common separated values (CSV) files allowing for further analysis in database, spreadsheet, and graphing programs (Figure 4B). 041b061a72