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colomoto / bioLQM

toolkit for the manipulation and analysis of Logical Qualitative Models of biological regulatory networks
http://colomoto.org/biolqm
GNU Lesser General Public License v3.0
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Support CIF format #21

Open sthiele opened 4 years ago

sthiele commented 4 years ago

Hi, I saw that bioLQM is supporting the SIF format. I've been switching from SIF to CIF (complex interaction format) for my application. To enhance the interoperability with other tools that use SIF i was thinking about writing a CIF2SIF converter. I saw that you also support Boolean formats which are very close to CIF. So i was wondering whether you are interested in implementing CIF support in bioLQM?

aurelien-naldi commented 4 years ago

Hi, I'm not sure what you saw, as bioLQM does not support SIF as SIF would be well suited for a list of interactions while bioLQM needs fully defined functions. If it can be useful, I'm interested in integrating more formats. Can you tell me a bit more about what you store in CIF exactly and how it can be mapped to a Boolean model?

sthiele commented 4 years ago

Sorry, I don't know how i came to the impression that bioLQM supports SIF. Apart from that thank you for your interest. The CIF format is in practice used to describe logical networks through a set of interactions that define target variables on the right hand side (similar to the BoolSim format). A -> B means A influences B . If multiple interactions are define for a variable, for example 

A -> C
B -> C.

these are cooperative influences which are usually interpreted as disjunction AvB≡C. The expression on the left hand side can include conjunction and negations such that !A & B -> C translates to ¬A∧B≡C. What sets CIF apart from other representation of Boolean networks is the ? operator which is used to express unknown influences ?A -> B could be interpreted as Av¬A≡B. When using the ?, the goal is usually to find a specialization that satisfies the observation data.