BioSigNet has been tested in Windows (98, XP, 2000) and Linux(RedHat 9.0). Click on a link below to download the system in compressed format. Unpacked the file into a directory of your choice and run the SigNetW.exe (or SigNet-linux in Linux) program.

Windows (2.11MB): You may need install Java Runtime Environment .

Linux (659KB): In addition to this, you also need to compile smodels and lparse. Also, make sure that you have Pearl and Java Runtime Environment.

How to use the interface

There are 7 tab panels: Knowledge base, Alphabet, Dynamic, Static, Trigger, Inhibition and Query. Knowledge base is for normal file operations. Alphabet is for editing action and fluent symbols. The next 4 tabs are for editing rules of knowledge base. Query is for editing and computing queries.

Move between items in a list using mouse. To add/delete items in a list, right-click on the list to bring up a popup menu with Add/Delete choices.

The lists in Alphabet are independent. In the tabs for rules, the information display in the lists are parts of a rule. In Dynamic, by moving (with mouse) between items in the Action-Direct Effect list, you can browse dynamic causal rules. Similarly, you can browse static causal rules by moving in the Effect list in Static tab, triggering rules by moving in Action list in Trigger tab, inhibition rules by moving in Action list in Inhibition tab. In these tabs, a text field at the bottom displays the rule being viewed.

To add a dynamic causal rule " a causes f if f_1, f_2, ..., f_n ", first add the pair (a,f) of action and effect in the Action-Direct Effect list. Then add the fluent literals f_1, f_2, ... f_n in the Precondition list.

To add a static causal rule " f_1, f_2, ..., f_n causes f ", first add f in the Effect list, then add the fluent literals f_1, f_2, ... f_n in the Precondition list. Similar logic is applied to the cases of triggering and inhibition rules: first you add the action in the Action list, then add the fluent literals in the Precondition list.

In Query tab, you can enter observations, select actions to be interventions, and select fluents that are assumed to be unknown. You can browse the entered observations by moving in the Time list. The following information is display in the figure below.

intervention  introduce(mutant(traf)).

unknown  mutated(traf).

initial  t0.

t0  precedes  t1.

bind(alpha_tnf,rec_tnf)  occurs_at  t0.

bound(nf_kappa_b,i_kappa_b)  at  t0.

Q =  always  ¬bound(fadd,procasp)  from  t0.

Press on the button Predict, Explain or Plan to compute the query  predict Q,  explain  Q, or  plan  Q.

Please contact N. Tran for any technical questions.