<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 15 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.E-MailFormatvorlage20
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 2.0cm 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple style='word-wrap:break-word'><div class=WordSection1><p class=MsoNormal>Hi Andy (Law),<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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! <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>You might be interested to also have a look at the other open source projects that were created around those topics:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/NucleicAcidSequenceTranslation4J">https://github.com/omnaest/NucleicAcidSequenceTranslation4J</a><o:p></o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/FASTQ4J">https://github.com/omnaest/FASTQ4J</a><o:p></o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/FASTA4J">https://github.com/omnaest/FASTA4J</a><o:p></o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/VCF4J">https://github.com/omnaest/VCF4J</a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/UniProt4J">https://github.com/omnaest/UniProt4J</a><o:p></o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/KEGG4J">https://github.com/omnaest/KEGG4J</a><o:p></o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/IUPHAR4J">https://github.com/omnaest/IUPHAR4J</a><o:p></o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/GPCRDB4J">https://github.com/omnaest/GPCRDB4J</a><o:p></o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/TCDB4J">https://github.com/omnaest/TCDB4J</a><o:p></o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/HMDB4J">https://github.com/omnaest/HMDB4J</a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><a href="https://github.com/omnaest/PMC4J">https://github.com/omnaest/PMC4J</a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>The projects are from my point of view prototypes as I do not maintain fixed release cycles, <o:p></o:p></p><p class=MsoNormal>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).<o:p></o:p></p><p class=MsoNormal>So they scale from very small devices up to large cloud clusters easily.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>If you should be interested to join forces at some point let me know…<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>In 2018 I created a short presentation, the slides you can find at:<o:p></o:p></p><p class=MsoNormal><a href="https://drive.google.com/open?id=1FpTI-D5ayh8lc44zTRvwsTrCumLwe_5V">https://drive.google.com/open?id=1FpTI-D5ayh8lc44zTRvwsTrCumLwe_5V</a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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:<o:p></o:p></p><p class=MsoNormal><a href="https://drive.google.com/open?id=1E1LvFVqGaJ4PUB5gwAg_Pisa9-MlDP33">https://drive.google.com/open?id=1E1LvFVqGaJ4PUB5gwAg_Pisa9-MlDP33</a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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.…<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Best regards,<o:p></o:p></p><p class=MsoNormal>Danny<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=DE>Von:</span></b><span lang=DE> Dev <dev-bounces@ensembl.org> <b>Im Auftrag von </b>LAW Andy<br><b>Gesendet:</b> Montag, 1. Februar 2021 11:49<br><b>An:</b> Ensembl developers list <dev@ensembl.org><br><b>Betreff:</b> Re: [ensembl-dev] Ensembl4J<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>If only there were funding... <o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><a href="http://jensembl.sourceforge.net/">http://jensembl.sourceforge.net/</a> <o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Later,<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Andy<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On 1 Feb 2021, at 10:24, Andy Yates <<a href="mailto:ayates@ebi.ac.uk">ayates@ebi.ac.uk</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>This email was sent to you by someone outside the University.<br>You should only click on links or attachments if you are certain that the email is genuine and the content is safe.<br><br>Hi Danny,<br><br>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.<br><br>Andy<br><br>------------<br>Andrew Yates - Genomics Technology Infrastructure Team Leader<br>The European Bioinformatics Institute (EMBL-EBI)<br>Wellcome Genome Campus<br>Hinxton, Cambridge<br>CB10 1SD, United Kingdom<br>Tel: +44-(0)1223-492538<br>Fax: +44-(0)1223-494468<br>Skype: andy.yates.ebi<br><a href="http://www.ebi.ac.uk/">http://www.ebi.ac.uk/</a><br><a href="http://www.ensembl.org/">http://www.ensembl.org/</a><br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>On 30 Jan 2021, at 17:42, <<a href="mailto:danny.kunz@gmx.de">danny.kunz@gmx.de</a>> <<a href="mailto:danny.kunz@gmx.de">danny.kunz@gmx.de</a>> wrote:<br><br>Hi Andy,<br><br>thanks for the response.<br><br>Don't worry, we have enough capacity to maintain what we need for our use cases.<br><br>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...<br><br>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.<br><br>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?<br><br><span lang=DE>Best regards,<br>Danny<br><br>-----Ursprüngliche Nachricht-----<br>Von: Dev <</span><a href="mailto:dev-bounces@ensembl.org"><span lang=DE>dev-bounces@ensembl.org</span></a><span lang=DE>> Im Auftrag von Andy Yates<br>Gesendet: Mittwoch, 27. </span>Januar 2021 12:04<br>An: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>Betreff: Re: [ensembl-dev] Ensembl4J<br><br>Dear Danny,<br><br>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.<br><br>Best regards,<br><br>Andy<br><br>* Ensembl did maintain a number of projects written in Java but these have been either retired or replaced over the past 10 years<br><br>------------<br>Andrew Yates - Genomics Technology Infrastructure Team Leader The European Bioinformatics Institute (EMBL-EBI) Wellcome Genome Campus Hinxton, Cambridge<br>CB10 1SD, United Kingdom<br>Tel: +44-(0)1223-492538<br>Fax: +44-(0)1223-494468<br>Skype: andy.yates.ebi<br><a href="http://www.ebi.ac.uk/">http://www.ebi.ac.uk/</a><br><a href="http://www.ensembl.org/">http://www.ensembl.org/</a><br><br><br><o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal>On 26 Jan 2021, at 10:50, <<a href="mailto:danny.kunz@gmx.de">danny.kunz@gmx.de</a>> <<a href="mailto:danny.kunz@gmx.de">danny.kunz@gmx.de</a>> wrote:<br><br>Hi all,<br><br>I have a quick question:<br><br>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.<br><br>Is there any interest from ensemble org side, that the java open source library “Ensembl4J” is maintained in the future?<br><br><a href="https://github.com/omnaest/Ensembl4J">https://github.com/omnaest/Ensembl4J</a><br><br>Best regards,<br>Danny Kunz<br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info:<br><a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></p></blockquote><p class=MsoNormal><br><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br><br><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></p></blockquote><p class=MsoNormal><br><br>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></p></div></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div></div><p class=MsoNormal>The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. <o:p></o:p></p></div></body></html>