I have a manuscript for a scientific publication, the data, and the scripts used to generate the result figures and tables. How can I wrap these three in an executable research compendium, so that others can easily reproduce the computational steps my study?
The best way is to use our online ERC user interface at
https://o2r.uni-muenster.de/. There you can upload a zip file of your workspace, which must include an R Markdown file that executes your workflow. You may choose to start you analysis from raw data or, if that takes very long, based on some pre-processed data.
The UI has a self-explanatory creation wizard guiding you through the process. Note that all your files will be publicly available on our demo server after your creation, and that you will need an ORCID account to log-in. New registrations are manually checked before you are allowed to upload any files, so please let us know if you're in a hurry.
You can also "manually" create an ERC as described in this guide that is part of the ERC technical specification.
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For a personal work I try to automate the workflow of my machine learning model but I face some question in the perspective of a professional approach.
At the moment I am doing the following tasks manually:
From the raw data I extract the data that interests me in a directory with the help of a third party software (to which I give in argument the parameters of the extraction).
Then I run another software, or in some cases one (or more) of my scripts (python) in order to pre-process my data which will be stored in a new directory.
Finally I provide the processed data to one of my model which returns the labeled data and that I store in a last directory.
process diagram of the previous description.
Each step (extract, pre-process and model) are always executed in the same order but I change the scripts/software parameters/model according to my needs or the comparison I need to do.
All my scripts are stored in an ordered script directory and the third party software is called from the command line from a python script.
My goal would be to have a script/software that does the whole loop by itself. As input it would take the raw data (or the directory where they are stored) and the different parameters to make the loop with the desired module (and their right parameters).
The number of module and parameter combinations is so big that I can't make a script for each one, that's why I want to build something very modular.
I can code myself my own script but I would like to have a more professional approach as if I had to implement it for a company.
My questions: In my case (customizable/interchangeable module) would it be more appropriate to use a framework (e.g. Kedro or any other) or to build it myself (because my needs are too specific)? If frameworks are appropriate which ones to choose (and why) ?
I've been researching frameworks that already exist but besides the fact that I'm not sure if they fit my needs there are so many that I'd like to spend some time on one that could help me in my future project or professional experience.
thanks you
We are developing a provide and register web service for CCDAs. Our vendor requires ADT as the patient registration portion. I can create a bare ADT message from the information provided to me in the CCDA in order to simplify the onboarding process (eliminate a dedicated ADT feed) and reduce the cost. BUT there are data elements (NK1, IN1, GT) that are either not included in the CCDA or not as robust.
I wanted to know if there are any documented data gaps between these two message (CCDA vs. ADT).
I wanted to get feedback to my approach.
I wanted to know the governing process for CCDA, as it makes sense to eventually include some of these ADT data points in the CCDA.
Thanks!
I don't think there is any specific documentation on data gaps between C-CDA and HL7 V2.x ADT messages. Generally it's fine to extract content from C-CDA and use that to construct an ADT message, but obviously you won't get everything. Governance is handled by the Structured Documents workgroup; anyone is welcome to join and submit change proposals.
May be you can find the additional information at CDA sections entries. C-CDA does not requires, for example, a CDA document to contain an immunizations sections with entries, but yes it defines how to include this information. If your CDA includes that information, that may be a good option.
Martí
Remember that CDA/CCDAs are not a replacement for clinical or administrative messages. Your approach is fine, but StrucDoc may push back on adding content that is directed toward workflow concerns. CDAs are static objects, they are not intended to trigger action.
As Marti points out, consider what information is possible the specific document you are using ... Or in the base CCDA specification. As long as your document template does not exclude a base specification section, that section can be included in a instance of that document template.
Without appropriate details it's hard to say for certain.
Does the system requiring ADT need encounters? In that case, you're going to need an encounters section from the CDA, which then needs to be turned into multiple A08s.
Do they just need demographics? That's probably do-able.
I would ask for specs around what event types they expect and what fields are required (or at least will bomb out on their side), and just go through the list a sample C-CDA or two on your side.
I work for a small healthcare company. We use a simple browser-based gui to create our healthcare claims. Recently our number of claims has grown. To make things easier, we'd like to be able to batch bill our claims now. We only do 1 type of procedure (this requirement will not change for the foreseeable future). I need to generate an 837I file for said procedure.
Any resources to learn about building an edi file as well as any walkthroughs about how I can do this for one procedure? I'm not looking for an already created solution. I'm also not looking to buy anything. I'm not looking to create a full x12 parsing tool.
We already have a solution for receiving acknowledgements and remittance advice. However, we don't have a simple way to batch upload unless we create 837 formatted files. This is only for one procedure so I'm looking to do this myself and learn as I go along.
I find entering the data in the feature file of specflow very painful specially when it is repetitive and large data. Can we use an external data source like spreadsheet to enter this data and then use this external datasource in the feature file?
It's theoretically possible, but probably so much effort that you wouldn't want to do it.
The problem is that the feature file is simply a human readable form. When it is saved in Visual Studio it is parsed and converted into the feature.cs file and that is the one that is compiled and used for testing.
So your process would become
edit spreadsheet
export to feature file
get specflow's VS plugin to convert to feature.cs
run msbuild
run tests via Nunit or similar
I wouldn't do this. Instead I'd focus on getting my tests to be better examples. It sounds like you are to trying to exhaustively cover every possibility. Don't come up with examples to cover every possible case, but instead cover as much logic as possible with fewer tests.
I have existing java code and need to create Design Document based on that.
For starter even if I could get all functions with input / output parameters that will help in overall proces.
Note: There is not commeted documentation on any procedures, function or classes.
Last but not least. Let me know for any good tool which will reduce time required for this phase. As currently we write every flow and related stuffs.
What you want is just too much. Quoting Linus Torvalds: “Good code is its own best documentation.”. Anyway, I digress.
You might want to look into UML tools which generate class/sequence diagrams from the code. There are many of them but only a handful support reverse engineering (into and from the class diagram), and even fewer subset support the same to/from sequence diagram. I only know MagicDraw could do this, but I am biased as I used to work for the manufacturer of this tool so do your shopping around first.
Use java docs: http://www.oracle.com/technetwork/java/javase/documentation/index-137868.html
or Introspection: http://docs.oracle.com/javase/tutorial/reflect/class/classMembers.html