Welcome

[Michael Hunger]

Welcome to the Neo4j-Biotech Google Group,

feel free to discuss everything related to graph databases and applications and projects from the biology domain, from proteins, reactome and genome sequences to ontologies and systematics.

If you join the group, please introduce yourself and your project and then feel free to explore the archives and collaborate in any ongoing discussions.

Looking forward to cool discussions of which I will probably only understand a tiny fraction - but that's what this group is all about, would love to see much more bio-domain specific lingo here than in the other tech-groups
I'm listening in.

I'm Michael Hunger, part of the Neo4j community team and actually a Jack of all Trades in Neo Technology. I love technology and science and always enjoy discussions (also meta) on those subjects. Feel free to address me with any
Neo4j or tech-specific questions.

Cheers

Michael

[Peter Neubauer]

Michael,
this is exciting. There has been a lot of interesting projects around
BioTech, will be extremely cool to see this group growing!

Cheers,

/peter neubauer

G: neubauer.peter
S: peter.neubauer
P: +46 704 106975
L: http://www.linkedin.com/in/neubauer
T: @peterneubauer

Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html

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[Thilo Muth]

Hello,
would start to introduce myself: As being a 2nd year PhD student in bioinformatics I am eagerly interested in graph databases and the combination with biology and biotech. My PhD supervisor Prof. Lennart Martens proposed the organization of the workshop "Graph Databases in Life Sciences" which
will be held on 12 nov in Ghent (Belgium), where I will be giving a talk in the morning session on the work I am doing as PhD project related
to proteomics and graph databases in combination.
In the afternoon, I will guide you through a workshop session which will be focussing on the integration of the human pathway and protein interaction database "Reactome" into the graph database system of neo4j.

Apart from that my further interests are software development (Java and C++ since 5+ years), cloud computing (topic of diploma thesis) and Kent Becks XP and pair programming. Finally, a lot of biology stuff which can be used from the "nerd" point of view. ;-)

As Michael proposed, we can start also a discussion on this and related topics prior to the workshop, so feel free to ask questions or comments on that,
the workshop schedule can be found online here:
http://www.meetup.com/graphdb-belgium/events/81881472/

Michael and me will keep you up to date the upcoming weeks until the event is being fired up. :-)

Looking forward to see you all in beautiful Ghent soon.

Cheers,
Thilo

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[Peter Neubauer]

That is cool Thilo,
and the meetup is filling up. Maybe we could have targeted meetups in
different cities to start with?

Cheers,

/peter neubauer

G: neubauer.peter
S: peter.neubauer
P: +46 704 106975
L: http://www.linkedin.com/in/neubauer
T: @peterneubauer

Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html

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[Rik Van Bruggen]

I cross posted to the dutch group a while ago. Will do the same in the other groups today.

Rik

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Rik Van Bruggen
r...@neotechnology.com
Mob: + 32 478 686800
Phone: +44 20 3286 2230
Skype: rvanbruggen

As a friend of Neo, register for GraphConnect and get a 20% discount. Code: GCFON

[ppa...@era7.com]

Hi everyone,

I'm Pablo Pareja and I work as Bioinformatics consultant/developer/researcher at Oh no sequences!, the R&D department of Era7 Bioinformatics.

It's already been more than 2 years since I started using Neo4j for bioinformatics and biological data modeling in general, being our company pioneer on using Neo4j graph database technology in this field.

It's been a long way since then and I have had time to develop many different projects and solutions around graph databases and Neo4j. 

The most important of them would probably be Bio4j "a bioinformatics graph based DB including most data available in UniProt KB (SwissProt + Trembl), Gene Ontology (GO), UniRef (50,90,100), RefSeq, NCBI taxonomy, and Expasy Enzyme DB. (Manuscript in preparation)" 

Just to give you a head's up of how much BigData is here you have some numbers:

• Number of Relationships: 717.484.649
  
• Number of Nodes: 92.667.745
  
• Relationship types: 144
  
• Node types: 42
  

Bio4j is also used together with some of our key projects such as BG7 (a bacterial genome annotation system. PLOS ONE 2012 in Press) and MG7 (a new system for the massive analysis of sequences from metagenomics samples specially designed for Next Generation Sequencing technologies. Manuscript in preparation). In the case of MG7, we are modeling extra information that is then attached to the existing data in Bio4j through the NCBI taxonomy tree. You can find more information about all this in the Wiki site of the project.

But not only that, I also used Neo4j for other projects/solutions such as Microsatellites modeling, NGS data storage, GO-protein annotations visualizations/ data exploration, sequence assembly... and much more!

Well, I'm realizing that I could be talking for ages about what we have already done with graph databases and Neo4j in particular but I don't want to get you bored with a huge message so let me know if you're interested in something in particular that we do.

Ahh, I forgot to mention two more things, one of our strong points when using Neo4j and graph DBs is how we use Cloud Computing (specifically AWS) in all the projects we may need it (which in the end means kind of all of them :D ), giving us many benefits such as scalability or easy data distribution.

And the other important thing is our very strong commitment with the Open Source movement, being ALL we do at Oh no sequences! 100% open source and released under AGPLv3 license.

Well, that's it for now, but please don't hesitate to ask me any questions/doubts/remarks you may have about all this, I will gladly answer it ;)

Cheers,

Pablo

PS: By the way, I'd like to bring this question up again in case someone could answer it here. I posted it about a month ago in the Neo4j group but didn't get any answer back for the last messages: https://groups.google.com/forum/?fromgroups#!topic/neo4j/oyOGrwO9i2g (it's about Using neo4j spatial for sequence indexing )

[Michael Lappe]

Hi everyone - 

My name is Michael Lappe and I have been working on different aspects of protein interaction networks and protein structures for a couple of years. Having experienced the difficulties of analysing connected biological data in classical RDMS first hand made me realize that biomolecular networks and neo4J is a match made in heaven (well, or in Malmö, actually). 

So far I have just been scratching the surface of neo4J and am just starting a new position at CLC bio in Denmark.

In case you'd like to read a bit more on my background and previous work, here are some links: 

my blog: cistronic.wordpress.com 

company home : http://www.clcbio.com/ 

some publications: http://www.molgen.mpg.de/~lappe/publications.html

twitter: @cistronic 

Happy hacking and looking forward to the meeting in Gent!  cheers .\\ichael 

Dr. Michael Lappe, Ph.D.

Senior Bioinformatics Scientist -

Functional Genomics and Systems Biology

CLC bio

Finlandsgade 10-12

Katrinebjerg

8200 Aarhus N

Denmark

Company Home: http://www.clcbio.com/

Developer Relations: http://connection.clcdeveloper.com/

Developer Related mail:develo...@clcbio.com

Mail: mla...@clcbio.com

Skype: michael.lappe.clcbio

[Peter Neubauer]

Hi,

I am Peter Neubauer and inventor and co-founder of Neo4j. I love to support OSS and connect people, project and places. If you need support or help from me - pay in Latte and Blog posts :)

Cheers,

/peter neubauer

G:  neubauer.peter
S:  peter.neubauer
P:  +46 704 106975
L:   http://www.linkedin.com/in/neubauer
T:   @peterneubauer

Neo4j 1.8 GA - http://www.dzone.com/links/neo4j_18_release_fluent_graph_literacy.html

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