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AnIML / techniques

AnIML Technique Definitions
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Open source converters #6

Open chambm opened 5 years ago

chambm commented 5 years ago

Do they exist to convert from vendor formats to aniML? Or at least from other open formats (mzML)? In dire need of some example documents too. Example documents section on website says: "Please contact the AnIML working group if you are interested in obtaining example documents." and then when I click "Contact" it says "Error - Category not found". :(

ghost commented 5 years ago

To my knowledge there are no open source converters available - at least not yet. I am currently working on a library to read / write AnIML files which could be used as a basis for open source converters.

The error on the animl.org webpage is exactly the same for me. Would be nice if someone fixed it. Maybe you can contact one of the guys listed on https://animl.org/contacts

burkhardschaefer commented 5 years ago

Thanks for pointing out the broken link. That is now fixed.

Most converters are closed source at this time (200+ instrument models). I'm aware of two efforts looking at a JCAMP-DX to AnIML converter as open source. Not sure how far along they are. We're thinking about collecting a wish list of instruments people need support for. We could then approach the vendor or create a 3rd-party implementation.

sneumann commented 5 years ago

I'd like to support that open source components can help increasing AniML adoption. I can buy only so much proprietary software, but I could look at/try all the Open Source software I want (and have time for ...). And I can't integrate the proprietary code into open tools, there is more to it than just parsing XML. The "Contact us for more" is quite an entry barrier users/developers might not bother with. Just my 2c. Yours, Steffen

ghost commented 4 years ago

My OpenSource AnIML library (.net Standard 2.0 based) is now in an alpha state where it is already possible to read, write and validate AniML documents. I have created some example documents and an example application that covers some of the most used elements as Samples, ExperimentSteps, ValueSets (AutoIcremented, Encoded, Individual) using fake data but they should do the job for testing purposes. So if anyone is interested in testing please drop me a message and I‘ll get back to you asap.

LabObjects commented 4 years ago

Hi - would be interested to help test your library. IS there a Url for the repo?

ghost commented 4 years ago

As the library in in alpha status the repo is currently private and will be made public as soon as the project is in beta status. I would provide a NuGet package with the library + an example application as separate project for the beginning. How can I contact you? As I do not want to publish my mail address here you could also send me a DM via Twitter @thomas_eigner

LabObjects commented 4 years ago

how about linkedin?

LabObjects commented 4 years ago

In the spirit of open source is would be preferable if you post the repo. Thanks. :-)

ghost commented 4 years ago

LinkedIn is also ok: https://de.linkedin.com/in/thomas-eigner-224458116 Well sure OpenSource is about making the sourcecode acccessible to the public but I will only do this when the project is in a state where it's ok for me to do this (and when I have decided which OpenSource license I will use). Until then it's a "private public alpha test" if you think OpenSource is incorrect ...

sneumann commented 3 years ago

Hm, as thomas_eigner seems to have left, is anyone picking up the OpenSource AnIML library ? Yours, Steffen

Mailaender commented 3 years ago

I thought about writing a converter for the @OpenChrom project, but there is not very much public information about this standard available. Please https://lablicate.com/about/contact us so we can exchange example files.

Mailaender commented 2 years ago

Sadly, I never received any example files. Nonetheless, I wrote converters from what is publicly available:

They will be shipped with https://lablicate.com/platform/openchrom and can therefore be used to convert proprietary vendor data in the realm of chromatography.