What is the Security Risk Assessment Tool (SRA Tool)?
The Office of the National Coordinator for Health Information Technology (ONC) recognizes that conducting a risk assessment can be a challenging task. That's why ONC, in collaboration with the HHS Office for Civil Rights (OCR) and the HHS Office of the General Counsel (OGC), developed an SRA Tool to help guide you through the process. This tool is not required by the HIPAA Security Rule, but is meant to assist providers and professionals as they perform a risk assessment. Please refer to the Security Risk Assessment Tool page for SRA Tool download link.
The SRA Tool takes you through each HIPAA requirement by presenting a question about your organization's activities. Your 'yes' or 'no' answer will show you if you need to take corrective action for that particular item. There are a total of 156 questions.
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. License: Public Domain. 4973 total downloads. Last upload: 5 years and 6 months ago. The SRA Toolkit contains multiple 'format'-dump commands, where format is the file format the SRA data is converted to abi-dump, fastq-dump, illumina-dump, sam-dump, sff-dump, and vdb-dump. One of the most commonly used commands is fastq-dump: $ fastq-dump options inputreads.sra. An example of running fastq-dump on Crane to convert SRA. . NOTE:- This app doesn't run on Virtual Devices (exclude Bluestacks). If you're using Nox Player, please change to Bluestacks instead to use this.
This tutorial also contains a section on how to use the sratoolkit (prefetch and fastq-dump) efficiently (bottom of the. The SRA toolkit and configure. Convert SRA to FASTQ format. To convert the example data to FASTQ, use the fastq-dump command from the SRA Toolkit on each SRA file. To install SRA Toolkit click here. R can be used to construct the required shell commands and to automate the process, starting from the SraRunInfo.csv' metadata table, as follows.
Resources are included with each question to help you:
- Understand the context of the question
- Consider the potential impacts to your PHI if the requirement is not met
- See the actual safeguard language of the HIPAA Security Rule
You can document your answers, comments, and risk remediation plans directly into the SRA Tool. The tool serves as your local repository for the information and does not send your data anywhere else.
Completing a risk assessment requires a time investment. At any time during the risk assessment process, you can pause to view your current results. The results are available in a color-coded graphic view (Windows version only) or in printable PDF and Excel formats.
For details on how to use the tool, download the SRA Tool User Guide [PDF - 4.9 MB].
A paper-based version of the tool is also available:
*Persons using assistive technology may not be able to fully access information in this file. For assistance, contact ONC at PrivacyAndSecurity@hhs.gov.
The Security Risk Assessment Tool at HealthIT.gov is provided for informational purposes only. Use of this tool is neither required by nor guarantees compliance with federal, state or local laws. Please note that the information presented may not be applicable or appropriate for all health care providers and organizations. The Security Risk Assessment Tool is not intended to be an exhaustive or definitive source on safeguarding health information from privacy and security risks. For more information about the HIPAA Privacy and Security Rules, please visit the HHS Office for Civil Rights Health Information Privacy website.
NOTE: The NIST Standards provided in this tool are for informational purposes only as they may reflect current best practices in information technology and are not required for compliance with the HIPAA Security Rule's requirements for risk assessment and risk management. This tool is not intended to serve as legal advice or as recommendations based on a provider or professional's specific circumstances. We encourage providers, and professionals to seek expert advice when evaluating the use of this tool.
상세 컨텐츠
NOTE: The NIST Standards provided in this tool are for informational purposes only as they may reflect current best practices in information technology and are not required for compliance with the HIPAA Security Rule's requirements for risk assessment and risk management. This tool is not intended to serve as legal advice or as recommendations based on a provider or professional's specific circumstances. We encourage providers, and professionals to seek expert advice when evaluating the use of this tool.
상세 컨텐츠
본문 제목
How To Use Sra Toolkit For Mac
본문
Installation and Settings Guideline. The right after guideline will outline for you the download, installation, and configuration of the SRA Toolkit.
Detailed information relating to the usage of individual equipment in thé SRA Toolkit cán become found on the tool-specific documents webpages. The NCBI SRA Toolkit enables reading ('dumping') of sequencing files from the SRA database and writing ('launching') files into the.sra structure (Notice that this is certainly not needed for distribution). The Toolkit supply code is usually offered in the form of the, and may end up being created with GCC. Nevertheless, pre-built software executables are usually obtainable for Linux, Windows, and Macintosh OS Times, and we highly recommend using these pre-buiIt executables whenever feasible. Downloading and setting up the SRA TooIkit. If you are using a internet browser, the using page contains download links to the nearly all current edition of the tooIkit for each óf the supported systems: SRA Toolkit downIoad page:.
If yóu are usually instead working from a command line interface, you may usé FTP or wgét to get the software program from the subsequent directory website: 'Instance: wget 'Unpacking thé Toolkit. Unix: tár -xzf sratoolkit.currént-centoslinux64.tar.gz.
Mac pc OSX: Double-cIick on the.tár.gz document and the Store Application will unpack it. Alternatively, command-line tar will also work (discover Linux example, above). Windows: use an archiving and compression utility (y.gary the gadget guy., Winzip, 7-Diddly, etc.), or simply double-click on the.squat document and move the 'sratoolkit.'
FoIder to the favored install area. Note: For many users, the Toolkit features (fastq-dump, sám-dump, etc.) wiIl not be located in their. This may require providing directory information about the area of the Toolkit. See the below good examples for how 'fástq-dump' would be called in various circumstances:. /username/srá-toolkit/fástq-dump The TooIkit 'trash can' listing has become positioned in the user-specified index 'sra-toolkit'./fástq-dump The TooIkit components are usually the in the current working website directory. fastq-dump lf the toolkit area is not described in your $PATH variable, then the Operating-system cannot locate the fastq-dump plan, even if it is certainly in the present directory. Take note: Windows users should end up being able to enter just 'fastq-dump.éxe' if you have navigated to the Toolkit 'rubbish bin' directory site.
Testing the Toolkit Settings The Toolkit comes with a default configuration that will work for most users. You may elect to perform the adhering to assessments to confirm that your configuration is functioning properly. The default area for the 'download database' is:.
Linux: /home/username/ncbi/public. Macintosh OSX: /Users/username/ncbi/public.
Home windows: C: Users username ncbi open public Be aware that if the tests fail, or if you wish to specify the download location for documents found from NCBI, yóu should configure yóur Toolkit set up. During normal operation, the Toolkit may end up being required to download the using varieties of information to the default location:.
Research sequences: Little (nearly all less than 70 MB) sequences used to decompress aligned SRA information. SRA data documents: If data are downloaded 'on-demand' using the toolkit, after that partial and whole SRA datasets (nearly all are many Gb in dimension) can become located right here. Take note: Manually down loaded SRA information obtained making use of a internet browser, wget, ascp, ór FTP may end up being stored anyplace in the local file program. For the check, we are using an human judgements dataset, (RNA-Seq (polyA+) evaluation of DLBCL mobile series HS0798), from the National Cancer Company's Cancer Genome Characterization Effort (CGCI) Task. It is a fairly small SRA dataset that includes lined up (reference-compressed) information, permitting us to test multiple elements of the toolkit concurrently. Open a airport terminal or order fast and 'compact disc' into the website directory containing the toolkit executables (at the.gary the gadget guy., downloadlocation/sratoolkitversion/trash can/).
Linux/Macintosh OSX:./fastq-dump -X 5 -Z SRR390728. Windows: fastq-dump.exe -X 5 -Z . SRR390728. If profitable, the check should connect to NCBI, download a little amount of information from SRR390728 and the benchmark sequence required to extract the information, and stream the very first 5 spots of the file ('-A 5' choice) to the screen ('-Z .' option).
If the settings is not really valid, an mistake like the using will likely be shown: fastq-dump.2.x err: product not found while setting up within virtual database component - the route 'SRR390728' cannot end up being opened as data source or desk'. If you receive an mistake like the one above, make sure you configure the toolkit (explained in the following section).
If you possess already configured the toolkit but are still incapable to finish the check successfully, make sure you email with a complete description of actions taken and error messages obtained. Configuring the Toolkit If you are using SRA Toolkit edition 2.4 or higher, you should run the configuration tool, situated within the bin subdirectory of the Toolkit bundle. Move to the 'rubbish bin' subdirectory for thé Toolkit and run the following command word:./vdb-config -i This tool will setup yóur download/cache area for downloaded data files and referrals. A screen will open up and existing the screen beneath. The configurations displayed right here have the default beliefs.
Of main importance is certainly the Workspace Place, which by default is in the ncbi website directory within your home index. If you possess enabled remote entry (allowed by default), thé toolkit will contact NCBI on demand over HTTP to get the documents it requires to full your instructions. In order for your commands to complete effectively, the toolkit desires sufficient free of charge space. Genomics datasets are usually very large; you may require 100's i9000 of GB of free of charge space. This is certainly the major issue when selecting the Work area Location. Perform you possess enough free space there for what you plan to do? If you need to alter the Work area Place, use the tab key to proceed the cursor (proven red here) to the modification button and press space or enter.
This will provide up the file navigation discussion (see below). If you already understand the path to the directory, you may usé the Goto switch to straight enter that path.
As soon as you have got entered or navigated to the appropriate directory, push tab to obtain to the Fine switch to return to the prior screen. Once you are usually content with the settings, use the tab key to obtain to the Save switch and press enter or space.
Press enter or room one even more time, then tab to the Get out of key and push enter or room. You will after that be came back to your covering command prompt.
Project maintained by Hosted on GitHub Pages - Theme.
What is the Protection Risk Evaluation Tool (SRA Tool)? The identifies that performing a risk evaluation can end up being a challenging task. That's why ONC, in collaboration with the HHS Workplace for Civil Rights (OCR), developed a downloadable Safety Risk Evaluation (SRA) Device to assist help you through the procedure. The device is made to assist healthcare providers carry out a safety risk assessment as needed by the HIPAA Protection Guideline and the Facilities for Medicare and Medicaid Assistance (CMS) Electronic Wellness Report (EHR) Motivation Plan.
Install Sra Toolkit
All information entered into the SRA Device is kept in your area to the customers' pc or pill. HHS does not get, collect, see, store or transmit any details moved into in the SRA Tool. The results of the assessment are displayed in a review which can be utilized to determine risks in plans, processes and systems and strategies to mitigate disadvantages are provided as the user is performing the evaluation. The focus on audience of this device is moderate and small providers; thus, use of this device may not really be appropriate for bigger institutions. The up to date edition of the popular Security Danger Evaluation (SRA) Device was released in October 2018 to create it less complicated to use and use more extensively to the dangers of the confidentiality, reliability, and accessibility of wellness information. The device layouts HIPAA Security Rule shields and provides enhanced features to document how your business implements safeguards to mitigate, or programs to reduce, identified risks. The fresh SRA Tool is accessible for Windows computer systems and notebooks.
However, the earlier iPad version of the SRA Tool is nevertheless available from the (lookup undér 'HHS SRA TooI'). The tool is now more user friendly, with useful new features like:. Improved user user interface. Modular workflow. Custom assessment reasoning. Progress tracker.
How To Use Sra Toolkit For Mac Download
Dangers vulnerabilities ranking. Detailed reports. Business associate and asset tracking.
Sra Toolkit Usage
General improvement of the consumer encounter For information on how tó use the device, download the. Make sure you keep any questions, remarks, or feed-back about the SRA Device making use of our. This includes any difficulty in using the device or troubles/bugs with the program itself. Also, please experience free to depart any suggestions on how we could improve the tool in the potential future. Legacy Version: Security Risk Evaluation Tool Version 2.0 Still making use of the previous version of the device? Note that you can't directly transfer data from 2.0 to 3.0, but can upload particular portions (e.g., lists of possessions and BAs). Réfer to the.
fór even more information.People using assistive technology may not be able to completely access info in this document. For help, contact ONC at. The Safety Risk Assessment Tool at HealthIT.gov will be supplied for educational purposes only. Make use of of this tool will be neither required by nor warranties conformity with federal government, condition or regional laws. Make sure you note that the information shown may not be suitable or appropriate for all wellness care suppliers and institutions.
The Security Risk Evaluation Tool can be not designed to be an inclusive or defined resource on safeguarding health info from personal privacy and security risks. For even more details about the HIPAA Personal privacy and Protection Rules, make sure you visit the.
Take note: The NIST Standards supplied in this tool are for informational purposes only as they may reveal current greatest methods in information technology and are usually not required for conformity with the HIPAA Protection Rule's needs for risk assessment and danger administration. This device is not really intended to function as legal assistance or as recommendations based on a supplier or expert's specific conditions. We motivate companies, and experts to look for expert guidance when analyzing the use of this tool.
I have set up making use of this command sudo apt-gét install sra-tooIkit under ubuntu. Now I feel trying to use oné of it'h part - fastq-dump.2.1.7 but I obtain an error from which l understoodthat l didn't spécify route to that software. This is usually weird because I can verify the edition of this software program and it is usually also added to /usr/rubbish bin/ listing. Will anyone understand how to overcome this error?
Code is usually below mkosinski@mkósinski-E540:$ fastq-dump.2.1.7 /WCO/Kasia/SRR1294095.sra 2015-10-19T20:52:13 fastq-dump.2.1.7 err: path incorrect while starting manager within data source module - neglected /house/mkosinski/WCO/Kásia/SRR1294095.sra Written 0 spots complete mkosinski@mkósinski-E540:$ fastq-dump.2.1.7 -edition fastq-dump.2.1.7: 2.1.7 mkosinski@mkosinski-E540:$ ls -d /usr/trash can/fastq-dump.2.1.7 -rwxr-xr-x 1 basic basic 93384 cze 15 2012 /usr/rubbish bin/fastq-dump.2.1.7.