Tag Archives: .net programming

Case Study 1: Stand Alone Satellite Office Solution

Integrated Into Sponsor’s Clinical Data Management (CDM) Environment

Anayansi gamboa - offshore Panama Data management

 

 

 

 

The Scenario:

The Sponsor was in need of a data management team to function in an integrated manner as an extension of the Sponsor’s CDM team. Based on geographic and offices constraints, coupled with the large volume of work, hiring individual contract resources on-site was not an option.

RA eClinica Solution:

  • RA eClinica Data Management Operations collaborated with Sponsor to develop CDM metrics, collaboration model and workflow, enabling the team to work across 3+ protocols
  • RA eClinica provided a full solution of 5+ CDM resources, project management, dedicated secure facilities integrating into Sponsor’s eClinical and CDMS databases.

Ra eClinica Results:

  • Develop of a long-term, efficient and cost-effective CDM solution.

RA eClinica is a established consultancy company for all essential aspects of statistics, clinical data management and EDC solutions. Our services are targeted to clients in the pharmaceutical and biotech sector, health insurers and medical devices.

The company is headquarter in Panama City and representation offices with business partners in the United States, India and the European Union. For discussion about our services and how you can benefit from our SMEs and cost-effective implementation CDISC SDTM clinical data click here.

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Project Plan: CDISC Implementation

CDISC standards have been in development for many years. There are now methodologies and technologies that would make the transformation of non-standard data into CDISC-compliance with ease. Clinical trials have evolved and become more complex and this requires a new set of skills outside of clinical research – Project Management.

As with many projects, CDISC is a huge undertake. It requires resources, technology and knowledge-transfer. The industry (FDA for example) has been working on standardization for years but on September 2013, it became official, in which the FDA released a ‘Position Statement‘.

So what is CDISC? We can say that it is way of naming convention for XPT files, or field names naming conventions or rules for handling unusual data. Currently, there are two main components of CDISC: SDTM (Study Data Tabulation Model) and aDAM (Analysis Data Model).

As a project manager and with the right tool, you can look to a single source project information to manage the project through its life-cycle – from planning, through execution, to completion.

1) Define Scope: This is where you’re tested on everything that has to do with getting a project up and running: what’s in the charter, developing the preliminary scope, understanding what your stakeholders need, and how your organization handles projects.

The scope document is a form of a requirement document which will help you identify the goals for this project. It can also be used as a communication method to other managers and team members to set the appropriate level of expectations.

The project scope management plan is a really important tool in your project. You need to make sure that what you’re delivering matches what you wrote down in the scope statement.

2) Define Tasks: we now need to document all the tasks that are required in implementing and transforming your data to CDISC.

Project Tasks  (Work packages) Estimates (work unit)
Initial data standards review 27
Data Integrity review 17
Create transformation models 35

The work breakdown structure (wbs) provides the foundation for defining work as it relates to project objectives. The scope of work in terms of deliverables and to facilitate communication between the project manager and stakeholders throughout the life of the project. Hence, even though, preliminary at first, it is a key input to other project management processes and deliverables.

3) Project Plan: Once we completed the initiation phase (preliminary estimates), we need to create a project plan assigning resources to project and schedule those tasks. Project schedules can be presented in many ways, including simple lists, bar charts with dates, and network logic diagrams with dates, to name just a few. A sample of the project plan is shown below:

project plan sample
image from Meta‐Xceed paper about CDISC

4) Validation Step: Remember 21 CFR Part 11 compliance for Computer Systems Validation? The risk management effort is not a one-time activity on the project. Uncertainty is directly associated with the change being produced by a project. The following lists some of the tasks that are performed as it pertains to validation.

  • Risk Assessment: Different organizations have different approaches towards validation of programs. This is partly due to varying interpretations of the regulations and also  due to how different managers and organizations function. Assess the level of validation that needs to take place.
  • Test Plan: In accordance with the project plan and, if not, to determine how to address any deviation. Test planning is essential in:  ensuring testing identifies and reveals as many errors as possible and to acceptable levels of quality.

test plan-cdisc

  • Summary Results: This is all the findings documented during testing.

An effective risk management process involves first identifying and defining risk factors that could affect the various stages of the CDISC implementation process as well as specific aspects of the project. riskplan

5) Transformation Specification: Dataset transformation is a process in which a set of source datasets and its variables are changed to  meet new standard requirements. Some changes will occur during this step: For example, variable name must be 8 chars long. The variable label must not be more than 40 chars in length. Combining values from multiple sources (datasets) into on variable.

6) Applying Transformation: This is done according to specification however, this document is active during the duration of a project and can change. There are now many tools available to help with this tasks as it could be time consuming and resource intensive to update the source code (SAS) manually. Transdata, CDISCXpres, SAS CDIDefine-it; just to name a few.

7) Verification Reports: The validation test plan will detail the specific test cases that need to be implemented  to ensure quality of the transformation. For example, a common report is the “Duplicate Variable” report.

8) Special Purpose Domain: CDISC has several special purpose domains: CO (comments), RELREC (related records or relationship between two datasets) and SUPPQUAL (supplemental qualifiers for non-standards variables).

9) Data Definition Documentation: In order to understand what all the variables are and how they are derived, we need a annotation document. This is the document that will be included during data submission. SAS PROC CONTENTS can help in the generation of this type of metadata documentation. The last step in the project plan for CDISC implementation is to generate the documentation in either PDF  or XML format.

CDISC has established data standards to speed-up data review and FDA is now suggesting that soon this will become the norm. Pharmaceuticals, bio-technologies companies and many sponsors within clinical research are now better equipped to improve CDISC implementation.

Need SAS programmers? RA eClinica can help provide resources in-house / off-shore to facilitate FDA review by supporting CDISC mapping, SDTM validation tool, data conversion and CDASH compliant eCRFs.

Disclaimer: The legal entity on this blog is registered as Doing Business As (DBA) – Trade Name – Fictitious Name – Assumed Name as “GAMBOA”.

Central Designer : Custom Function

A few days ago I received an interesting mail from M. Gupta from my other personal website EDC Developer in which Gupta asked: “Custom Function not working. Hi Anayansi, I have developed a custom function in C# for Central designer but looks like it is not even executing could you please share the steps to create and deploy the custom function”.

First of all, sorry it took me a little longer to respond. My time is limited and I don’t often get this kind of emails from my EDC Developer personal site (this website is for recruiters / potential clients for consulting assignments). Here at {EDC} Developer wordpress, I shared knowledge-based and industry related practices.

anayansigamboa - c# programming
image credit courtesy of Google

Before you can start rules programming in Central Designer, you must make sure you have the following rights assigned to you:

Study Rule Design (either as a study designer or rule writer):

  • Import User-defined functions
  • Define/modify data entry rules
  • Define/modify constants

Some companies assigned a group of people to write rules (rule writers but without access to other modules/features in CD) and the study designer is in charged of the eCRF study build (forms design). That way, while a study designer is building a form, the rule programmer can start edit checks/rule programming activities on other forms.

Remember the custom functions are programs written outside Central Designer. Functions allow you to encapsulate a piece of code and call it from other parts of your code. You may very soon run into a situation where you need to repeat a piece of code, for multiple visits for example, and this is where functions come in.

You will need Visual Studio or C#. Once you program and test your code and assuming it is working, you can load it onto CD (see user rights and refer to the annotated eCRF).

Example: Query rules may not run as expected on initial submissions for an itemset, if there is a calculation rule that sets the value on an item in a different visit, and the calculation rule is attached to the same form as the query rule.

In a previous article about troubleshooting in CD, I discussed some ways to troubleshoot rules. It will give you some insights about what to check when a rule is not working.

Something else to consider during rule development:

  • Source control your code and binaries using VSS or similar tools.
  • dll versioning may cause existing functions to stop working.
  • You can deploy functions on a study or library level. Any changes will affect other studies.
  • Remove anything that is not being referenced
  • Try using Try-Catch
  • Remember to reference CD (still called PhaseForward or see other functions provided by Oracle/PhaseForward during the initial installation) still under the old name – PhaseForward
  • Unit test (extensively) in a test environment

Rules Unit Testing:

  • Turn on rule tracing in the InForm event log
  • Check the log (warnings / errors can give you some clues that something is not right with an edit check calling this new custom function
  • Write and run test cases for data-entry rules, global conditions or workflow rules (this is very important)

Now we are ready for testing in InForm (this requires deployment).

And if it all else fails, try this article about Learn How to Avoid The 10 Most Common C# Mistakes.

Good luck and thank you for connecting.

Comments? Please post it below.

Anayansi Gamboa, MPM, an EDC Developer Consultant and clinical programmer for the Pharmaceutical and Biotech industry with more than 13 years of experience.

Available for short-term contracts or ad-hoc requests. See my specialties section (Oracle, SQL Server, EDC Inform, EDC Rave, OpenClinica, SAS and other CDM tools)

(Beginners) Learn .NET and c# in 60 days – Lab 5 (Day 1)

FAIR USE-
“Copyright Disclaimer Under Section 107 of the Copyright Act 1976, allowance is made for “fair use” for purposes such as criticism, comment, news reporting, teaching, scholarship, and research. Fair use is a use permitted by copyright statute that might otherwise be infringing. Non-profit, educational or personal use tips the balance in favor of fair use.”

(Beginners) Learn .NET and c# in 60 days – Lab 4 (Day 1)

FAIR USE-
“Copyright Disclaimer Under Section 107 of the Copyright Act 1976, allowance is made for “fair use” for purposes such as criticism, comment, news reporting, teaching, scholarship, and research. Fair use is a use permitted by copyright statute that might otherwise be infringing. Non-profit, educational or personal use tips the balance in favor of fair use.”

Tip #3 – Become an Expert at Debugging

Studies have shown that we spend 50% of our time debugging, but only learn debugging by trial and error. This webcast by John Robbins was in the top 10 favorites on Microsoft web site, and it is a real goldmine. Watch this 4-hour webcast on debugging, and you are bound to save many times that in the future. Here is the handout for the webcast – be sure to download the source code for the Visual Studio macros. John Robbins is the co-founder of Wintellect and the author of several books on .NET Debugging.

Check out http://idealprogrammer.com/ if you are new to VB.NET or ASP technology.