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Old 10-27-2014, 02:13 AM   #1
pekrau
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Location: Stockholm, Sweden

Join Date: Feb 2011
Posts: 3
Default Any suggestions for order portal web system?

Hi all,

I'm at NGI Sweden https://portal.scilifelab.se/genomics/, a genomics facility primarily for Swedish academics. We have a Drupal-based system for our users to describe and submit their sequencing orders to us.

For various reasons, we are looking for alternatives, and I was wondering if anyone has ideas or suggestions.

Our wish list for the system:
  1. Allow a user to submit an order, and to view his/her previous orders.
  2. Allow approx 1,500 users, 500 projects per year, 6 coordinators, 3 sites (current numbers, will increase).
  3. The order may be very complex, requiring hierarchical choices (e.g. if technology X, then library prep Y, then analysis Z).
  4. An order may have to be created in increments, saving it between sessions.
  5. Have a proper API, both for read and write, e.g. for updating the state of order using info from the lab.
  6. Allow non-programmers to modify the forms data, e.g. which library prep protocols are available, etc.
  7. Allow any kind of change of the form fields, without screwing up previously submitted forms.
  8. Possible to run severnal different instances of the portal (for different platforms) which are completely distinct, *except* for the user accounts, which should be common.

We have looked at various Cloud-based form tools such as http://www.formassembly.com/, but apart from several technical shortcomings, we have a problem in that our data may have to reside on in-house servers due to policy.

There are many reasons why our current Drupal solution is not optimal. One is that changing the form fields is non-trivial, and it is sometimes hard to remove options, due to backwards-compatibility issues. There are other things which make us dislike Drupal, and although it works, we wish to find something better.

Are there any good Open-Source systems for this? Or how do people solve this problem?

Yours,
Per Kraulis
NGI Sweden, SciLifeLab
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Old 11-13-2014, 09:47 AM   #2
fbidu
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Location: Campinas, Brazil

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Hello Per Kraulis,

I'm a software developer in Brazil and I'm doing an internship in a NGS facility here. When I was hired, they assigned me the task to create a whole system that includes most of the features you pointed out plus stock and financial managing and lab notebook.

As of now, I've mapped the workflow of the facility - I have no previous background in genomics or bioinformatics - and I'm evaluating the options: to create a brand new system or to use an existing one? The most interesting system I found was GNomEx (http://hci-scrum.hci.utah.edu/gnomexdoc/). It seems to fulfill most of our needs but I'm having a hard time putting it to work.

If we don't find that GNomEx completes all our needs, we will develop a new system. It will probably be open source, but I have no idea when we will finish it - probably within the next year
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Old 11-14-2014, 05:34 AM   #3
pekrau
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Hi fbidu,

Thanks for the information. I have looked at little at GNomEx.

1) It seems to cover a larger part of the workflow than we need, since we already have a working LIMS and data processing pipeline.
2) I couldn't find much info on how the site admin (or project coordinator) can change the fields for specifying the samples, libprep and other request details.

So although it looks useful, I'm not sure if this is a good fit for us.

We are still discussing at our lab how to move forward. One possibility is to use FormAssembly, but that does not seem to keep the order for the customer to look at. Its model is that the form is submitted once and for all by the customer, never to be seen again by her, which is not really how we want it.

/Per K
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Per Kraulis, Ph.D.
Systems Architect, National Genomics Infrastructure (NGI), SciLifeLab.
Dept Biochemistry and Biophysics, Stockholm University.
[email protected], +46 (0)8 5248 1465, http://www.scilifelab.se/
Visiting address: Tomtebodavägen 23A, Karolinska Institutet Science Park, Solna
Mailing address: SciLifeLab Stockholm, Box 1031, 171 21 Solna, Sweden
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Old 01-21-2015, 06:27 PM   #4
Genohub
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Location: genohub.com

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Hi Per,

Through Genohub, 1-4, 6 are possible from your wish list. While Genohub is not an open source option, you can list services in a tiered fashion allowing users to select sequencing read lengths, read numbers or coverage required along with the type of library prep construction they need: https://genohub.com/shop-by-next-gen...ncing-project/. We take this input information and display packages that match these requirements.

You can have several coordinators with different authorizations login and manage incoming projects. There are no limits to the number of projects you can have going at the same time or the number of logged in users.

Orders and order information is always saved. Before a user submits a project they can save it and share it with collaborators. At every stage of a project you can communicate with the user. All communication, data uploads and project information is displayed in a single stream. You or the user can always go back to projects that have been completed. They are stored for reference purposes.

You sign up for an account to give it a try: https://genohub.com/ngs-providers/. We'd like to hear what you think. Contact us at [email protected] to see if we can better tailor this service to your needs.
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Old 01-22-2015, 12:54 AM   #5
pekrau
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Location: Stockholm, Sweden

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Thanks for your reply. I will have a look at this, although we have already decided to code our own solution, see https://github.com/pekrau/OrderPortal
__________________
Per Kraulis, Ph.D.
Systems Architect, National Genomics Infrastructure (NGI), SciLifeLab.
Dept Biochemistry and Biophysics, Stockholm University.
[email protected], +46 (0)8 5248 1465, http://www.scilifelab.se/
Visiting address: Tomtebodavägen 23A, Karolinska Institutet Science Park, Solna
Mailing address: SciLifeLab Stockholm, Box 1031, 171 21 Solna, Sweden
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