Petra will be the caretaker of all things Biotech/LifeScience + Neo4j

[Michael Hunger]

Hello Everyone,

I want to introduce Petra Selmer a colleague of mine who has a background in biotech/life-science and works in our Cypher Language team while finishing her PhD on the side. We had a really great conversation after GraphConnect this week and agreed on that she would be a much better caretaker of the community working on biological/medical/chemical data and graphs than I am (because I'm clueless).

We discussed several things:

- presenting, documenting use-cases

- running (official) workshops (with submitted papers) and sponsorshops (or meetups) at biotech conferences

- look for collaborations with scientific institutions to extend Neo4j's capabilities with requirements for this community

- integrate and provide bio/chemical databases

We had a intro round for some projects a while back so it would be great if you'd share your project information again or updated us on your progress.

Have a great weekend,

Cheers, Michael

[Martin Preusse]

Hi Everyone,

great to hear that things move forward.

I have two projects:
- integration of public databases like ENSEMBL, RefSeq, UniProt, KEGG, Reactome etc
- integration of results from various omics technologies (e.g. to connect epigenomics and metabolomics)

I will drop out of academic research soon but I will stay in life science and connected to my current research institutions. And I'm pretty sure I will use neo4j in the future ;)

I'd be happy to support you or get involved in whatever is going to happen next. Especially in workshops/sponsorshops/meetups and collaborations with scientific institutions.

Cheers
Martin

Am Samstag, 9. Mai 2015 um 11:58 schrieb Michael Hunger:

> Hello Everyone,
>
> I want to introduce Petra Selmer a colleague of mine who has a background in biotech/life-science and works in our Cypher Language team while finishing her PhD on the side. We had a really great conversation after GraphConnect this week and agreed on that she would be a much better caretaker of the community working on biological/medical/chemical data and graphs than I am (because I'm clueless).
>
> We discussed several things:
> - presenting, documenting use-cases
> - running (official) workshops (with submitted papers) and sponsorshops (or meetups) at biotech conferences
> - look for collaborations with scientific institutions to extend Neo4j's capabilities with requirements for this community
> - integrate and provide bio/chemical databases
>

> We had a intro round for some projects a while back (https://groups.google.com/d/msg/neo4j-biotech/yCqh0E-gENU/iATxwPc9kT0J) so it would be great if you'd share your project information again or updated us on your progress.

>
> Have a great weekend,
>
> Cheers, Michael
>

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[Thilo Muth]

Dear Michael, dear Petra, hello everyone,

I am currently finishing my PhD project and have worked with several graph database "use cases" in the field of life sciences / bioanalytics / (meta)proteomics and glycomics. In 2012, Michael Hunger, my supervisor in Belgium and me have organized a workshop on graph database in the life sciences.

One of the main projects during the last 3,5 years was the development of a proteomics software pipeline for the analysis of microbial communities - which are

of importance for example in the production of methane in bio gas plants (renewable energy sources) and also in the human intestinal tract as our human body harbours one magnitude more microbial cell than human body cells. Basically, we used neo4j as flexible database backend in order to allow the user to write customized queries in Cypher.

If you are interested in the science, please have a look here:

http://www.ncbi.nlm.nih.gov/pubmed/25778831

If someone needs to have access to the paper - I can send it around, of course.

At the moment, as mentioned before - I am currently heavily stuck in writing the PhD thesis - apart from looking for jobs both in industry and academics. ;-)

Best regards,

Thilo

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[Petra Selmer]

Hi everyone

I am very happy to be taking on the challenge of being this community's caretaker! Thank you all so much for your responses.

A little bit about me: I am based in London, and have been working since October last year as a developer in the Cypher Language team at Neo Technology. I am also writing up my PhD (hopefully to submit in autumn/winter this year) in which I research ways in which a graph query language could allow for slight imprecisions, so users can explore complex domains without having to get everything exactly right in their query. My previous experience in the life sciences and health care domains comprise the development of a data management system for a new mental health and neurosciences research programme, as well as software for clinical trials and audits within the area of critical care.

Our intentions for this group are to raise awareness of Neo4j as a viable tool within the biotech and life sciences communities, thereby increasing the adoption of Neo4j.

To this end, we should very much like to know from you all which conferences or events are of interest and are relevant, and which of these have scope for potential sponsorship. Additionally, we are seeking collaboration opportunities. Also, we are very keen for you to talk about your projects - if you are able to do so - at your local meetup groups, and also, if possible, to share these; please let us know if we can help in any way.

We have been keeping an eye out for relevant upcoming conferences posted on the ACM Sigmod Dbworld site (https://research.cs.wisc.edu/dbworld/); I have detailed some of these below, in case they are of interest:

* Semantic Web applications and tools for Life Sciences (http://www.swat4ls.org/)

In particular, they also have a hackathon session (http://www.swat4ls.org/workshops/cambridge2015/programme/hackathon/). If you have a great idea which would fit, we would love to hear from you.

* International Congress for Conservation Biology and the European Congress for Conservation Biology (http://www.iccb-eccb2015.org)

* International Conference on Intelligent Systems for Molecular Biology and the European Conference on Computational Biology (http://www.iscb.org/ismbeccb2015)

* International Workshop on Network Tools and Applications for Biology and Integrative Bioinformatics International Symposium (http://www.igst.it/nettab/2015/)

* International Symposium on Network Enabled Health Informatics, Biomedicine and Bioinformatics   (http://hi-bi-bi.cpsc.ucalgary.ca/2015/)

* International Workshop on Data Mining in Bioinformatics (http://home.biokdd.org/biokdd15/)

* International Conference on Data Integration in the Life Sciences (http://www.isi.edu/events/dils2015/home)

Please also invite your colleagues or friends in the research area to join the group.

And, finally, please let me know if you need any help or support - we'll be very happy to help!

Best wishes

Petra

[Martin Preusse]

Hi Petra,

thanks for the introduction.

You mention that you are seeking collaboration opportunities. Could you elaborate what kind of collaboration you have in mind? Do you plan to support applications for biotech and life science somehow? I am always happy to work together, and I'm trying to spread neo4j in my local biotech community ;)

Martin

> > > Hello Everyone,
> > >
> > > I want to introduce Petra Selmer a colleague of mine who has a background in biotech/life-science and works in our Cypher Language team while finishing her PhD on the side. We had a really great conversation after GraphConnect this week and agreed on that she would be a much better caretaker of the community working on biological/medical/chemical data and graphs than I am (because I'm clueless).
> > >
> > > We discussed several things:
> > > - presenting, documenting use-cases
> > > - running (official) workshops (with submitted papers) and sponsorshops (or meetups) at biotech conferences
> > > - look for collaborations with scientific institutions to extend Neo4j's capabilities with requirements for this community
> > > - integrate and provide bio/chemical databases
> > >

> > > We had a intro round for some projects a while back (https://groups.google.com/d/msg/neo4j-biotech/yCqh0E-gENU/iATxwPc9kT0J) so it would be great if you'd share your project information again or updated us on your progress.

> > >
> > > Have a great weekend,
> > >
> > > Cheers, Michael

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[Petra Selmer]

Hi everybody

Martin, thanks very much for your email - I'll now answer your questions. 

What we are seeking in terms of collaboration is broadly as follows:

- We want to foster collaboration, exchange and discussions of people using Neo4j in their biotech projects. To this end, we are very keen to hold more workshops like this (so, something a bit more focussed than a meetup):  http://neo4j.com/blog/graph-databases-in-life-sciences-workshop/

- We want to introduce graph technology to the broader biotech audience, most of whom are still using relational stores for graph-structured data, or triple-stores (where we would like Neo4j to be considered as a viable alternative). To this end, we want to raise awareness at conferences.

In terms of immediate support for applications for biotech and life sciences:

- We should like to host publicly-available datasets - please let me know which ones would be useful.

- We are happy to promote and/or review papers using Neo4j, if this is something researchers would find helpful

Regarding the sponsorship of conferences, after some investigation by Michael and myself, we are thinking of exhibiting at the International and European Congress for Conservation Biology (http://www.iccb-eccb2015.org/) in Montpelier, France, August 2 - 6. However, neither of us is able to be present at this event, and we thought it would be great if someone from the community would volunteer to do this? We would cover the sponsorship fee, which includes free registration for one person, and a 50% discount for a second. Are any of you interested (and available) in doing this? If yes, please let me know! Also, if you have any questions about this, please ping them through to me too.

Best wishes

Petra