[ensembl-dev] Ensembl4J

Mon Feb 1 20:24:42 GMT 2021

Hi Andy (Law),

wow JEnsembl looks pretty well designed…I did a quick svn checkout and from what I see I bet a lot of work went into it! 

Super interesting as I also implemented a good bunch of the features documented on the JEnsembl project page. Seems as the implementation directions overlapped here a lot for the two projects.

You might be interested to also have a look at the other open source projects that were created around those topics:

https://github.com/omnaest/NucleicAcidSequenceTranslation4J

https://github.com/omnaest/FASTQ4J

https://github.com/omnaest/FASTA4J

https://github.com/omnaest/VCF4J

https://github.com/omnaest/UniProt4J

https://github.com/omnaest/KEGG4J

https://github.com/omnaest/IUPHAR4J

https://github.com/omnaest/GPCRDB4J

https://github.com/omnaest/TCDB4J

https://github.com/omnaest/HMDB4J

https://github.com/omnaest/PMC4J

The projects are from my point of view prototypes as I do not maintain fixed release cycles, 

nevertheless instead of the old mybatis those projects use a key document store abstraction and have adapters from native file system json files over a small nitrite database, mongodb and apache ignite (Hadoop, full in memory database and cache).

So they scale from very small devices up to large cloud clusters easily.

If you should be interested to join forces at some point let me know…

Also it might be relevant that our patient organization based research focus went already way further as our intention was to solve a group of closely related rare disease cases, so we ended up with a lot of application spikes:

In 2018 I created a short presentation, the slides you can find at:

https://drive.google.com/open?id=1FpTI-D5ayh8lc44zTRvwsTrCumLwe_5V

The main goal was a 3D metabolome visualization and flux simulation engine which integrated metabolome and genome information like receptors, transporters, enzymes but also drugs/ligands. The prototype was quite advanced, I still have a short video how it worked tracking an enzyme deficiency via a rough direction based on urine metabolite sampling:

https://drive.google.com/open?id=1E1LvFVqGaJ4PUB5gwAg_Pisa9-MlDP33

Unfortunately no official contact was willing to host the webapplication prototype even if they got the full working prototype (130 000 LOC) for free and I had the feeling that most contacts did not even look into it, so I got frustrated and went on at that point of time and removed the prototype from my hosting systems to save my time for more relevant topics.

Still I am a heavily included in research activity around Irritable Bowel Syndrome, so I would be willing to support also in other directions where it doesn’t take too much of my time, especially in exchange for contributions to my research project parts, which could also be non development related, like access to next gen sequencing or metabolomic services for some of our patients, study support or even small things like review of genome reports for conceptional errors or plausibility, contacts to researches on the same field etc.…

E.g. we also contributed about 2 years ago into a cancer mRNA analysis project, where we used a double probe mRNA sequencing with a statistical weighted token on the fly matching to investigate a colon carcinoma in the descending colon of a patient. The result was really fascinating, as we could provide a visualization and with that a theoretical explanation why butyrate inhibits cancer growth in vitro, as much more enzymes like the LDH were overexpressed like the butyrate CoA ligase which indicates that also those serve as primary energy provider for the cancer core.

So, if someone has an interest in supporting or being supported, don’t hesitate to let me know - Ensembl4J (and I assume also JEnsembl at that time) seems only being a small part on the way to bring all the genomic data Ensembl provided over the years to an effect for patients at the end of the line.

Best regards,

Danny

Von: Dev <dev-bounces at ensembl.org> Im Auftrag von LAW Andy
Gesendet: Montag, 1. Februar 2021 11:49
An: Ensembl developers list <dev at ensembl.org>
Betreff: Re: [ensembl-dev] Ensembl4J

If only there were funding... 

http://jensembl.sourceforge.net/ 

Later,

Andy

On 1 Feb 2021, at 10:24, Andy Yates <ayates at ebi.ac.uk <mailto:ayates at ebi.ac.uk> > wrote:

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Hi Danny,

Ensembl continues to be primarily a Perl based project but there is growing development in Python and JavaScript, which will continue to increase over the coming years.

Andy

------------
Andrew Yates - Genomics Technology Infrastructure Team Leader
The European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
Skype: andy.yates.ebi
http://www.ebi.ac.uk/
http://www.ensembl.org/

On 30 Jan 2021, at 17:42, <danny.kunz at gmx.de <mailto:danny.kunz at gmx.de> > <danny.kunz at gmx.de <mailto:danny.kunz at gmx.de> > wrote:

Hi Andy,

thanks for the response.

Don't worry, we have enough capacity to maintain what we need for our use cases.

If any feature requests for other api parts should come up in the future, we will see then at that point of time how we can distribute the work better or how we can attract more contributors...

As you have shown interest of the project being maintained and being available for consumers, I will enhance the documentation a little and will publish it to the maven central in the next weeks.

Just out of curiosity, if the java expertise of the ensembl teams has diminished in the last years, on which languages are you operating your pipelines and platforms?

Best regards,
Danny

-----Ursprüngliche Nachricht-----
Von: Dev < <mailto:dev-bounces at ensembl.org> dev-bounces at ensembl.org> Im Auftrag von Andy Yates
Gesendet: Mittwoch, 27. Januar 2021 12:04
An: Ensembl developers list <dev at ensembl.org <mailto:dev at ensembl.org> >
Betreff: Re: [ensembl-dev] Ensembl4J

Dear Danny,

We certainly support that you’ve developed the API and have made it available under an open source license. We also hope you can find others to help maintain the codebase, however Ensembl’s Java expertise* has diminished over the past years and is one of the reasons why we cannot offer our help to maintain this. We will continue to advertise any pending changes to our REST API and FTP site via our pre-release blog posts and attempt to minimise disruption to both of these resources.

Best regards,

Andy

* Ensembl did maintain a number of projects written in Java but these have been either retired or replaced over the past 10 years

------------
Andrew Yates - Genomics Technology Infrastructure Team Leader The European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
Skype: andy.yates.ebi
http://www.ebi.ac.uk/
http://www.ensembl.org/

On 26 Jan 2021, at 10:50, <danny.kunz at gmx.de <mailto:danny.kunz at gmx.de> > <danny.kunz at gmx.de <mailto:danny.kunz at gmx.de> > wrote:

Hi all,

I have a quick question:

We developed for our rare disease research some java based open source libraries including a first prototype for the ensembl REST API and FTP access.

Is there any interest from ensemble org side, that the java open source library “Ensembl4J” is maintained in the future?

https://github.com/omnaest/Ensembl4J

Best regards,
Danny Kunz
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