Re: [Neo4j] You are working with Neo4j and biology or biotech? I'd love to hear from you.

[Michael Hunger]

Hi Wolfgang & others,

the plan is to run a graphs in biotech workshop in Berkeley in January.

Kimmen Sjolander works on a project (phylo4j) to assemble loads of information (ontologies, genetic, proteins, pathways, etc) into a huge graph. https://dl.dropboxusercontent.com/u/14493611/phylo4j-cypher%20models.pdf

In the past we ran the Graphs in Life Sciences Workshop with Lennart Martens & Thilo Muth in Ghent, Belgium with lots of interesting contributions: http://blog.neo4j.org/2012/11/graph-databases-in-life-sciences.html
Esp. the metaproteonomics project by Thilo (source on google code, presentation in the blog was interesting). He also did a webinar last week: https://vimeo.com/77450061

There is also this nice GraphGist pathway model by Ben Butler-Cole: http://gist.neo4j.org/?24d0c8032389c7e52f9f (feel free to add your own models, it's simple)

And we started a (kind of quiet) google group for neo4j-biotech that I intended for people to discuss topic specific scientific details of their models and implementations. (http://groups.google.com/group/neo4j-biotech).

Michael

Am 26.10.2013 um 03:19 schrieb Wolfgang Hoeck <who...@me.com>:

> Hi Michael, met you @ GraphConnect in SF in Data Loading session. I am planning to introduce Neo4j to folks in my company within the Biotech/Pharma space in November. Would love to hear more about applications of Neo4j in this space. Anything you can share would be helpful. Biology is a highly connected data space, so graph databases should be able to have a great impact, but we have to be patient so we don't over promise and under deliver as seen too many times before. Just connecting data without a good model behind probably won't do :-)
>
> I can see applications in Competitive Intelligence, Business Process Modeling, System Configuration Management, Sample/Cell Line/Experiment Annotation System, Drug Target Database, etc.
>
> Many thanks in advance for any further insight in this space.
>
> --
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[Martin Preusse]

Good to know that neo4j found it’s way into biotech industry ;) I can imagine that it’s sometimes not easy to find a good model to store data a graph. I love using neo to store biological knowledge because the model comes so easy. 3 bil years of evolution (or god for that matter) developed it for us.

I taught some biologists to use cypher and it feels natural to them. Start with a gene, find associated pathways, but only show pathways with diabetes related genes.

What do you think would be most interesting for biotech/pharma? I suppose you could store all your super secret bio knowledge about drugs/targets/interactions etc and the advantage would be that it’s easier to access by other scientists and in general more flexible than other data bases. Kind of a knowledge base thing.

[Michael Hunger]

Martin,

sounds really interesting. Do you have a write-up/paper/article somewhere that explains how you interacted with/ taught the scientists and what the tools where that they used?
And what we can learn from giving them a tool like cypher (and what we can improve).

Good questions.

I've seen many use-cases:

- metabolic pathways
- drug research / individual patient therapy
- pattern finding in genome sequencing data
- modeling ontologies (opentreeoflife, phylo4j)
- aggregating biological databases (bio4j)
- tracing origins of samples to infer ecological processes (e.g. food chains)
- analysing scientific papers to get recommendations an better quality inference
- breeding / selection of organisms (both natural and genetically modified)

And there are hundreds more that I can imagine (and I'm a total layman in terms of biotech).

Cheers,

Michael

P.S: Moving this discussion to the neo4j-biotech group from now on :)

[Keiichiro Ono]

Hi.

I've been working with biologists for last 10 years, and our main
interest is how to integrate, analyze, and visualize biological
networks. I think there are three main graph database user community
in life science:

1. Biological network analysis
- This is the field I'm working on. Originally, PPI network data
sets were relatively small (~10K/species), but now we have tons of
new, large data sets (genetic interactions, etc.). This is why people
start using graph DB in this field.

2. Management of human-curated pathway/module data sets
- Such as KEGG or Reactome. Probably their actual implementations
are not using graph DB, but I'm sure they are the potential users.
(We've just started one recently with pharma, and it's backend is
graph DB: http://www.ndexbio.org/)

3. General biological knowledge representation (or Semantic Web)
- There is a large semantic web community in life science field.
EBI, one of the big player in bioinformatics field, recently released
official endpoints ( http://www.ebi.ac.uk/rdf/ )


I think ISB (https://www.systemsbiology.org/) already uses Neo4j, and
I've just started to use it in our project ( http://nexontology.org/
). Anyway, I'm sure there are tons of use cases. Now both backend
and frontend technologies are mature enough to implement very
complicated biologists' requirements, and that's the reason we start
using it. If there is an opportunity to share ideas and techniques in
this field, that would be great!

Thanks,
Kei

Cytoscape Consortium Core Developer
UC, San Diego Trey Ideker Lab
http://cytoscape.org/


2013/10/26 Michael Hunger <michael...@neotechnology.com>:

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--
Keiichiro Ono http://keiono.github.io/

[Keiichiro Ono]

[Michael Hunger]

Kei,

all these projects sound really interesting. Love the move towards graph databases in this field. I think we can gather a load of new insights from better technology here.

As you're working with cytoscape - is there any chance we could move a better integration between Cytoscape and Neo4j forward? Don't know about the integration points on your side?

Also as you're in the US, would you be interested to participate in the January workshop in Berkeley and speak about your projects?

Cheers,

Michael

[Kimmen Sjolander]

Michael -- thanks for reminding me about the Berkeley January meeting!

Everyone who is interested in coming to a one-day workshop in Berkeley in January should please contact me. We will focus on Neo4j databases for biological data, with particular emphasis on databases, methods, and visualization tools for 'omics data and analysis. We're developing tools to predict orthologs using phylogenetic tree analysis, predict protein-protein interactions ("interactomes", combining experimental data and bioinformatics methods), predict protein "function" and structure (integrating data from many large graphs over our trees and interactomes), construct functional association networks (from transcriptomics data), personal genomics, cancer genomics and metagenomics/metatranscriptomics. 

We're interested in bringing together any developers who are interested in participating in this effort. Please feel free to forward this to people who you think would like to participate.

My lab has been developing bioinformatics databases and webservers since 1997, and we have a huge relational database (in Postgres) that we call PhyloFacts. (You're welcome to use it -- it's available online.) PhyloFacts has ~7M proteins from bacteria, archaea and eukarya (animals, plants, fungi, etc.) placed into ~93K phylogenetic trees for protein superfamilies. Our Postgres database is a little over a terabyte, but that's because it doesn't include all proteins in the major databases. Once we include those data, we can expect to expand to ~10TB.  Our database includes data from many third-party databases (e.g., metabolic pathways, interactions, orthology relationships, Pfam domains, taxonomy, 3D structure) so there is heterogeneous metadata for many members and experimental or manually curated data for a very small fraction. We want to be able to use the connectivity in our trees to help us mine that data, but Postgres, it turns out, is not ideal for searching large trees.  We're starting to build a Neo4j database for our PhyloFacts trees, using Bio4j as a starting point. We call our new database "Phylo4j".

Phylo4j is funded by an EAGER (Exploratory research) grant from the National Science Foundation; it will be an open source project, and our hope and expectation is that it will be used by biologists worldwide to support their research.

We are looking for collaborators on this project. We are currently collaborating with the Bio4j group in Granada, Spain (led by Pablo Pareja) and building on Bio4j (adding new data types and methods). I am very happy to include any other members of the Neo4j developer community. If you're interested in getting involved, please contact me, and let me know if you're interested in either coming to Berkeley for the workshop or in joining remotely. (We hope to have teleconferencing capabilities.)   

I also have many international collaborators who would probably want to be involved (in the computational biology community -- many in London, Barcelona, Rome, Stockholm and Jerusalem. Is anyone on this list from the EU, and interested in getting involved in EU-based activities? I'll put you in touch with my collaborators.

-Kimmen

Kimmen Sjölander, Ph.D.
Professor, Department of Bioengineering
and Department of Plant and Microbial Biology
308C Stanley Hall #1762
University of California, Berkeley 94720
http://phylogenomics.berkeley.edu

[Keiichiro Ono]

Hi Michael.

Actually, I'm using Cytoscape-Neo4j importer/exporter (via Tinkerpop
Blueprints stack) internally to build/tweak backend database for our
web apps. It still needs a lot of work to release it as a complete
end-user app, but I want to publish it as an open source software. I
need to discuss this with our team members, but I'll try (just like
other scientific application developers, I need to do all of user
interview, design, coding, testing, and documentation...)

Also, I'm happy to present our work in Berkeley. Please let me know
about the details once available.

Thanks,
Kei



2013/10/26 Michael Hunger <michael...@neopersistence.com>:

[Martin Preusse]

Hi,

are there any news on the workshop in Berkeley? I live in Germany and can't come, but I'd join remotely if possible. Also a meeting/workshop in Europe would be great. 

Kimmen, you mentioned that you have many collaborators in Europe. I would be very interested to get in contact with the neo4j bio community and a meeting could be a good starting point.

I'm already using neo for all my work and we consider adopting it for more collaborations/projects.

Martin

[Keiichiro Ono]

I have the same question here...
Any updates on this event?

Thanks,

Kei
UC, San Diego School of Medicine
Trey Ideker Lab


2013/11/18 Martin Preusse <martin....@gmail.com>:

[Michael Hunger]

Afaik, Kimmen rescheduled it for February or April due to too much business from the grant application efforts.

Kimmen could you point out a short schedule / intent about the workshop? That would be great.

And please also answer Martins question about the collaboration.

Thanks,

and happy holidays to everyone.

Michael

[Keiichiro Ono]

Hi Michael.

Thank you for the updates.
No hurry, but maybe I'll have several international trips in April, so
please let me know when you have estimated dates.

Thanks again for organizing the workshop, and happy holidays!

Kei





2013/12/17 Michael Hunger <michael...@neopersistence.com>:

[Kimmen Sjolander]

Hi all,

Sorry for the long delay in replying. The fall semester was busier than usual, particularly due to a huge NIH grant proposal that consumed >3 months of my time, and I'm only now catching up on emails. 

Unfortunately, for several reasons including a heavy teaching load this spring, we'll need to push back the workshop to after the spring semester ends (mid-May). 

Michael, perhaps you and I should discuss the scheduling over the summer separately? Let me know your scheduling constraints for this summer. I have a few meetings to attend out of town over the summer. At present, the last two weeks of May and the first week of June are safe bets, but there are a few other weeks that are also possible.

-Kimmen

On Wed, Jan 8, 2014 at 8:46 AM, Alex Frieden <al...@frieden.org> wrote:

Hi all,

Just wanted to see if there was any update on this.  Thanks!

Alexander Frieden

[Eduardo Pareja Tobes]

Hey Michael, everyone

I just noticed the existence of this group; I'm one of the Bio4j people that Kimmen mentioned below. For anyone who doesn't know what this Bio4j thing is, check the slides from Pablo Pareja presentation at FOSDEM this past weekend: http://ohnosequences.com/slides/fosdem-2014/bio4j-bigger-faster-leaner. 

Good to see growing interest in this area, it's been ~4 years since we started working on Bio4j with Neo4j and we were starting to feel a bit lonely :) I do think that there are a lot of opportunities for collaboration in this space!

[Eduardo Pareja Tobes]

Hi Martin,

one of the Bio4j people, definitely get in touch with us! 

also think that organizing something in Europe would be nice (we're based in Spain)

[Michael Hunger]

Welcome Eduardo,

Pablo has been member of this group for a while I think. I started it after the workshop in Ghent (http://blog.neo4j.org/2012/11/graph-databases-in-life-sciences.html)

I definitely agree, that bio4j is really impressive in terms of technology and content (# of entries & merged databases).

(btw. did you know that Neo4j 2.1 which is currently worked on finally handles super-nodes in a much better way?)

Yesterday after the Munich Meetup, Martin Preusse (who's also on this list) asked me about about a re-run of the workshop.

One idea I had (besides the workshop that Kimmen wanted to organize) is to run it again in Europe (which is very strong in biotech). 

And probably co-locate the workshop with one of the biotech conferences? (Martin made some suggestions, e.g. the ones in Strasbourg or Bielefeld in September)

I would love to see more collaboration, that was the reason why I started this group. Unfortunately it has not taken up as I intended. 

Probably you are just all busy working and researching :)

Love to hear some ideas of you all - i.e. things you currently work on (that you can talk about) or ideas you have on what could be done better in your field by using graph databases.

Have a nice weekend,

Cheers, 

Michael

[Eduardo Pareja Tobes]

something went wrong with my reply, I’ll try to write more or less the same thing again; apologies in case of duplicates

Yeah I just saw that Pablo posted some messages here, you know sometimes a distributed team makes for some lack of communication :)

About the upcoming features in Neo4j 2.1, anything that can help with improving local indexing (and data locality in general) is really good news for us!

And organizing something in Europe is definitely a good idea. By Strasbourg in September I guess you mean the ECCB; that looks to me like a really good option. It is the biggest European conference in bioinformatics/computational biology, a lot of young people go there (which I think will be more receptive to the graph dbs in biology/biotech idea), and we’re going to be there anyway :)

cheers

[Martin Preusse]

@bio4j people: Yes, we talked about conferences and ECCB came to mind. Bielefeld is the German Conference for Bioinformatics, but ECCB makes more sense of course. Would be great to somehow dock a neo/bio meeting to it. 

I started looking into bio4j a while ago and it's really really impressive. I read about your cooperation with Kimmen. So far I haven't found more publications/projects making use of bio4j.

Would be very interesting to interact with you guys, preferably before September ;) I am getting closer to publish the first paper using neo4j.

Cheers

Martin

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[Thilo Muth]

Hey Pablo, Martin and all neo4j-biotech users,

having neo4j in biotech near to the ECCB would be great - so count me in.

The GCB is also a great conference - but not that popular internationally as the previous one of course. :)

Currently supervising a student in glycobiology / analysis and we will make heavy use of neo4j for his project on putting glycans and enzyme reactions into the database. Possibly, that would be something interesting to talk about - and of course the MetaProteomeAnalyzer software, which we will

try to publish within the next few months.

Are you guys planning one day for the meetup?

Cheers,

Thilo (the guy from the neo4j life sciences workshop in Ghent)

---

[Michael Hunger]

Let's organize a meetup in Bielefeld for GCB and then a workshop co-located with ECCB.

For GCB:

Are there german bio-tech meetup-groups / academic groups that we could reach out to and invite ?

Perhaps we can start to work out, if the meetup should be the day before the conference (Sep 28) or on one of the evenings (social events of the conf: http://www.gcb2014.de/index.php/social-eventsf). 

GCB is http://www.gcb2014.de/ from Sep 28 (workshops) Sep-29-Oct 1st, CfP deadline Mai 30

Perhaps we can even submit a workshop on "getting started with graph databases in life science" ? http://www.gcb2014.de/index.php/call-for-workshops

Michael

[Thilo Muth]

Hey,

both of them together - that is a great idea! :-)

GCB:

Could invite some people of Lennarts group (CompOmics group) in Ghent - remember that some of them were pretty interested in graph databases.

Also some people here in Magdeburg and university Jena (strong in bioinformatics) may be interested as well.

Note: However, crucial will be to come up with 4-6 regular papers for the workshop session:

"Workshops should cover at least a single session (4-6 regular papers). The workshop organizers should ensure registration and presence of authors of accepted papers."

As far as I remember from GCB in Göttingen last year, the Metaproteomics workshop didn't have that many papers presented.

Also we may discuss with the program chairs - stating that graph databases are hot brand new stuff and do not have a long history as boring genome sequence alignments for example. ;-)

I would care about the draft on the one-page description for the proposal - and send it to Michael / anyone who is interested to work on the orga.

Cheers,

Thilo

---

[Michael Hunger]

Cool, please do.

I have zero experience in biotech conferences but would be interested to learn.

Are the workshops full day? If so we could cover a variety of topics form intro to graphs, use-case in bio-tech, hands-on usage for concrete example from interesting domains.

Michael

[Thilo Muth]

Workshops were mostly half day last year:

http://www.gcb2013.de/workshops

It would depend on the confirmed speakers and papers.

Michael, do you still have a list of the attendees from the Ghent workshop in 2012?

Possibly, some of the have used neo4j in their research projects by now and are willing to come again / speak / write conference papers.

Best regards,

Thilo

---

[Martin Preusse]

GCB:
Sounds good, I think a workshop for GCB won't be a problem even with less papers. They are very happy about any interesting workshop, no? … I can help with the proposal and organization if necessary. And I can ask a few people in Munich. As far as I know only few attend GCB, but maybe I can get some of the network guys to join.

Given that proceedings are published in a German informatics journal, it will be harder to find somebody willing to contribute papers. On the other hand it's easier for e.g. Master students or pet projects.

ECCB:
Official workshop or private meetup? The workshop registration deadline was 24. jan: http://www.eccb14.org/guidelines/workshops I think we could still try but two official workshops don't make sense from the paper perspective. ECCB proceedings are published in Bioinformatics, which is of course a lot better than GCB.

So both have pros and cons, not sure which is better.


Martin

Am Freitag, 21. Februar 2014 um 10:31 schrieb Thilo Muth:

> Workshops were mostly half day last year:
> http://www.gcb2013.de/workshops
>
> It would depend on the confirmed speakers and papers.
>
> Michael, do you still have a list of the attendees from the Ghent workshop in 2012?
> Possibly, some of the have used neo4j in their research projects by now and are willing to come again / speak / write conference papers.
>
> Best regards,
> Thilo
>
>

> > Cool, please do.
> >
> > I have zero experience in biotech conferences but would be interested to learn.
> >
> > Are the workshops full day? If so we could cover a variety of topics form intro to graphs, use-case in bio-tech, hands-on usage for concrete example from interesting domains.
> >
> > Michael
> >
> > Am 21.02.2014 um 09:49 schrieb Thilo Muth <mu...@mpi-magdeburg.mpg.de (mailto:mu...@mpi-magdeburg.mpg.de)>:
> > > Hey,
> > >
> > > both of them together - that is a great idea! :-)
> > >
> > > GCB:
> > > Could invite some people of Lennarts group (CompOmics group) in Ghent - remember that some of them were pretty interested in graph databases.
> > > Also some people here in Magdeburg and university Jena (strong in bioinformatics) may be interested as well.
> > >
> > > Note: However, crucial will be to come up with 4-6 regular papers for the workshop session:
> > > "Workshops should cover at least a single session (4-6 regular papers). The workshop organizers should ensure registration and presence of authors of accepted papers."
> > >
> > > As far as I remember from GCB in Göttingen last year, the Metaproteomics workshop didn't have that many papers presented.
> > > Also we may discuss with the program chairs - stating that graph databases are hot brand new stuff and do not have a long history as boring genome sequence alignments for example. ;-)
> > >
> > > I would care about the draft on the one-page description for the proposal - and send it to Michael / anyone who is interested to work on the orga.
> > >
> > > Cheers,
> > > Thilo
> > >

> > > > Let's organize a meetup in Bielefeld for GCB and then a workshop co-located with ECCB.
> > > >
> > > > For GCB:
> > > >
> > > >
> > > > Are there german bio-tech meetup-groups / academic groups that we could reach out to and invite ?
> > > >
> > > > Perhaps we can start to work out, if the meetup should be the day before the conference (Sep 28) or on one of the evenings (social events of the conf: http://www.gcb2014.de/index.php/social-eventsf).
> > > >
> > > > GCB is http://www.gcb2014.de/ from Sep 28 (workshops) Sep-29-Oct 1st, CfP deadline Mai 30
> > > >
> > > > Perhaps we can even submit a workshop on "getting started with graph databases in life science" ? http://www.gcb2014.de/index.php/call-for-workshops
> > > >
> > > > Michael
> > > >
> > > >
> > > > Am 21.02.2014 um 08:30 schrieb Thilo Muth <mu...@mpi-magdeburg.mpg.de (mailto:mu...@mpi-magdeburg.mpg.de)>:
> > > > > Hey Pablo, Martin and all neo4j-biotech users,
> > > > >
> > > > > having neo4j in biotech near to the ECCB would be great - so count me in.
> > > > > The GCB is also a great conference - but not that popular internationally as the previous one of course. :)
> > > > >
> > > > > Currently supervising a student in glycobiology / analysis and we will make heavy use of neo4j for his project on putting glycans and enzyme reactions into the database. Possibly, that would be something interesting to talk about - and of course the MetaProteomeAnalyzer software, which we will
> > > > > try to publish within the next few months.
> > > > >
> > > > > Are you guys planning one day for the meetup?
> > > > >
> > > > > Cheers,
> > > > > Thilo (the guy from the neo4j life sciences workshop in Ghent)
> > > > >
> > > > >
> > > > >

> > > > > > @bio4j people: Yes, we talked about conferences and ECCB came to mind. Bielefeld is the German Conference for Bioinformatics, but ECCB makes more sense of course. Would be great to somehow dock a neo/bio meeting to it.
> > > > > >
> > > > > > I started looking into bio4j a while ago and it's really really impressive. I read about your cooperation with Kimmen. So far I haven't found more publications/projects making use of bio4j.
> > > > > >
> > > > > > Would be very interesting to interact with you guys, preferably before September ;) I am getting closer to publish the first paper using neo4j.
> > > > > >
> > > > > > Cheers
> > > > > > Martin
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > Am 12.02.2014 um 10:16 schrieb Eduardo Pareja Tobes <eduardo.pa...@gmail.com (mailto:eduardo.pa...@gmail.com)>:
> > > > > >
> > > > > > >
> > > > > > > something went wrong with my reply, I’ll try to write more or less the same thing again; apologies in case of duplicates
> > > > > > >
> > > > > > >
> > > > > > > Yeah I just saw that Pablo posted some messages here, you know sometimes a distributed team makes for some lack of communication :)
> > > > > > >
> > > > > > >
> > > > > > > About the upcoming features in Neo4j 2.1, anything that can help with improving local indexing (and data locality in general) is really good news for us!
> > > > > > >
> > > > > > >

> > > > > > > And organizing something in Europe is definitely a good idea. By Strasbourg in September I guess you mean the ECCB (http://www.eccb14.org/); that looks to me like a really good option. It is the biggest European conference in bioinformatics/computational biology, a lot of young people go there (which I think will be more receptive to the graph dbs in biology/biotech idea), and we’re going to be there anyway :)

> > > > > > >
> > > > > > >
> > > > > > > cheers
> > > > > > >
> > > > > > >
> > > > > > > On Friday, February 7, 2014 4:29:30 PM UTC+1, Michael Hunger wrote:
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > > Welcome Eduardo,
> > > > > > > >
> > > > > > > > Pablo has been member of this group for a while I think. I started it after the workshop in Ghent (http://blog.neo4j.org/2012/11/graph-databases-in-life-sciences.html)
> > > > > > > >
> > > > > > > > I definitely agree, that bio4j is really impressive in terms of technology and content (# of entries & merged databases).
> > > > > > > > (btw. did you know that Neo4j 2.1 which is currently worked on finally handles super-nodes in a much better way?)
> > > > > > > >
> > > > > > > > Yesterday after the Munich Meetup, Martin Preusse (who's also on this list) asked me about about a re-run of the workshop.
> > > > > > > >
> > > > > > > > One idea I had (besides the workshop that Kimmen wanted to organize) is to run it again in Europe (which is very strong in biotech).
> > > > > > > > And probably co-locate the workshop with one of the biotech conferences? (Martin made some suggestions, e.g. the ones in Strasbourg or Bielefeld in September)
> > > > > > > >
> > > > > > > > I would love to see more collaboration, that was the reason why I started this group. Unfortunately it has not taken up as I intended.
> > > > > > > > Probably you are just all busy working and researching :)
> > > > > > > >
> > > > > > > > Love to hear some ideas of you all - i.e. things you currently work on (that you can talk about) or ideas you have on what could be done better in your field by using graph databases.
> > > > > > > >
> > > > > > > > Have a nice weekend,
> > > > > > > >
> > > > > > > > Cheers,
> > > > > > > >
> > > > > > > > Michael
> > > > > > > >
> > > > > > > >
> > > > > > > > Am 07.02.2014 um 16:12 schrieb Eduardo Pareja Tobes <eduardo.pa...@gmail.com (JAVASCRIPT-BLOCKED-BLOCKED-blocked-blocked-blocked-blocked:)>:
> > > > > > > > > Hey Michael, everyone
> > > > > > > > >
> > > > > > > > > I just noticed the existence of this group; I'm one of the Bio4j people that Kimmen mentioned below. For anyone who doesn't know what this Bio4j thing is, check the slides from Pablo Pareja presentation at FOSDEM this past weekend: http://ohnosequences.com/slides/fosdem-2014/bio4j-bigger-faster-leaner.
> > > > > > > > >
> > > > > > > > > Good to see growing interest in this area, it's been ~4 years since we started working on Bio4j with Neo4j and we were starting to feel a bit lonely :) I do think that there are a lot of opportunities for collaboration in this space!
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Saturday, October 26, 2013 11:09:54 AM UTC+2, Michael Hunger wrote:
> > > > > > > > > > Hi Wolfgang & others,
> > > > > > > > > >
> > > > > > > > > > the plan is to run a graphs in biotech workshop in Berkeley in January.
> > > > > > > > > >
> > > > > > > > > > Kimmen Sjolander works on a project (phylo4j) to assemble loads of information (ontologies, genetic, proteins, pathways, etc) into a huge graph. https://dl.dropboxusercontent.com/u/14493611/phylo4j-cypher%20models.pdf
> > > > > > > > > >

> > > > > > > > > > In the past we ran the Graphs in Life Sciences Workshop with Lennart Martens & Thilo Muth in Ghent, Belgium with lots of interesting contributions: http://blog.neo4j.org/2012/11/graph-databases-in-life-sciences.html (http://www.google.com/url?q=http%3A%2F%2Fblog.neo4j.org%2F2012%2F11%2Fgraph-databases-in-life-sciences.html&sa=D&sntz=1&usg=AFQjCNHvRBQ7J76GcLa0Gf34I4sVQ-0KUg)

> > > > > > > > > > Esp. the metaproteonomics project by Thilo (source on google code, presentation in the blog was interesting). He also did a webinar last week: https://vimeo.com/77450061
> > > > > > > > > >
> > > > > > > > > > There is also this nice GraphGist pathway model by Ben Butler-Cole: http://gist.neo4j.org/?24d0c8032389c7e52f9f (feel free to add your own models, it's simple)
> > > > > > > > > >
> > > > > > > > > > And we started a (kind of quiet) google group for neo4j-biotech that I intended for people to discuss topic specific scientific details of their models and implementations. (http://groups.google.com/group/neo4j-biotech).
> > > > > > > > > >
> > > > > > > > > > Michael
> > > > > > > > > >
> > > > > > > > > > Am 26.10.2013 um 03:19 schrieb Wolfgang Hoeck <who...@me.com>:
> > > > > > > > > >
> > > > > > > > > > > Hi Michael, met you @ GraphConnect in SF in Data Loading session. I am planning to introduce Neo4j to folks in my company within the Biotech/Pharma space in November. Would love to hear more about applications of Neo4j in this space. Anything you can share would be helpful. Biology is a highly connected data space, so graph databases should be able to have a great impact, but we have to be patient so we don't over promise and under deliver as seen too many times before. Just connecting data without a good model behind probably won't do :-)
> > > > > > > > > > >
> > > > > > > > > > > I can see applications in Competitive Intelligence, Business Process Modeling, System Configuration Management, Sample/Cell Line/Experiment Annotation System, Drug Target Database, etc.
> > > > > > > > > > >
> > > > > > > > > > > Many thanks in advance for any further insight in this space.
> > > > > > > > > > >
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[Eduardo Pareja Tobes]

Hi everyone

GCB:

Sounds good to me too. Someone from our team is going to be based in Munich (LMU) from July to December collaborating around Bio4j and population genetics (an EU project) so we could help with that and speak about what we're doing there; so Thilo if you already started with the proposal I'd like to help! From the papers perspective is of course worse than the ECCB, but this could lead to a more informal and productive atmosphere. 

ECCB:

If you think that they could admit a workshop submission, then we should go for it. As I said before we're going anywhere so no problem, and I'm glad to help with the submission or anything else

best

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Eduardo Pareja-Tobes

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[Eduardo Pareja-Tobes]

sorry for the typo: “As I said before we’re going anyway so no problem” but anyway we’re OK with going anywhere too :)

Eduardo Pareja-Tobes

Math & CS freak

oh no sequences!

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