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djinnome
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labelled each lisp file, fixed results section
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‎BPS/ltms/abduction.lisp

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;; biohacker/trunk/BPS/ltms/abduction.lisp
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;; Ex 3, Chapter 10
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; a literal is a unique pair (<node> . <label>)

‎BPS/ltms/explain.lisp

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;; biohacker/trunk/BPS/ltms/explain.lisp
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(defun node->fact (node &aux literal)
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(setq literal
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(cond ((true-node? node) (tms-node-true-literal node))

‎BPS/ltms/forward-abduction.lisp

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;; biohacker/trunk/BPS/ltms/forward-abduction.lisp
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(defun keep-assuming (fact label patterns &key (debugging t) &aux all-assumed)
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(dolist (pattern patterns)
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(dolist (new-fact (fetch pattern))

‎metabolizer/biotransformation.lisp

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(setq *substrate-atom-bond-graph* (adj-list 'etoh))
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;((O (2 1) (3 1)) (H (1 1)) (C (1 1) (4 1)) (C (3 1)))
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;((O (2 1) (3 1))
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; (H (1 1))
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; (C (1 1) (4 1))
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; (C (3 1)))
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(setq *substrate-pattern* (adj-list '|Alcohols|))
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;((O (2 1)) (R (1 1)))
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;((O (2 1))
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; (R (1 1)))
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(setq *product-template* (adj-list '|an aldehyde|))
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;((H (4 1)) (O (4 2)) (R (4 1)) (C (1 1) (2 2) (3 1)))
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;((H (4 1))
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; (O (4 2))
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; (R (4 1))
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; (C (1 1) (2 2) (3 1)))
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(setq *product-atom-bond-graph* (adj-list 'acetald))
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;((O (3 2)) (H (3 1)) (C (2 1) (1 2) (4 1)) (C (3 1)))
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;((O (3 2))
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; (H (3 1))
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; (C (2 1) (1 2) (4 1))
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; (C (3 1)))
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(setq *pattern-substrate-bindings* (match-substrate-pattern *substrate-atom-bond-graph* *substrate-pattern*))
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; (#(HEAD 1 3 2 C H H H H H) (O R H))
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; (#(HEAD 1 3 2 C H H H H H)
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; (O R H))
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(cpd-adj-list-structure-equal? (*product-atom-bond-graph* (adj-list 'acetald))
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;
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;; For efficiency and error avoidance, match-kb without match-h should followed with match-single with match-h on query results.
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(defun match-substrate-pattern (substrate pattern &key (substrate-format :adj-list) (pattern-format :adj-list))
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(multiple-value-bind (pattern-atom-bond-graph
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substrate-atom-bond-graph
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‎network-debugger/loader.lisp

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;; biohacker/trunk/network-debugger/loader.lisp
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;; network-debugger.lisp should
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;; * define *nd-path*
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;; * load the BPS/utils/init

‎network-debugger/nd-extended-rules.lisp

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;; nd-extended-rules.lisp
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(rule ((:INTERN (enzyme ?enzyme . ?genes)))
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(let* ((actual-genes (remove :UNKNOWN ?genes))
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(unknown? (find :UNKNOWN ?genes))

‎network-debugger/nd-inter.lisp

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;; nd-inter.lisp
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(defstruct (nd (:PRINT-FUNCTION nd-print-procedure))
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title ; Pretty name
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ltre ; Pointer to its LTRE

‎network-debugger/nd-pathway-rules.lisp

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;; nd-pathway-rules.lisp
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(rule ((:INTERN (enzyme ?enzyme . ?genes)))
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(dolist (?gene ?genes)
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(rassert! (gene ?gene) :GENE-OF-ENZYME))

‎network-debugger/nd-rules.lisp

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;; biohacker/trunk/network-debugger/nd-rules.lisp
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(rule ((:INTERN (enzyme ?enzyme . ?genes)))
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(dolist (?gene ?genes)
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(rassert! (gene ?gene) :GENE-OF-ENZYME))

‎network-debugger/nd.lisp

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;; nd.lisp
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(defmacro network-debugger (name
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&key
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(debugging nil)

‎network-debugger/presentation/demo-experiments.lisp

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;;biohacker/trunk/network-debugger/presentation/demo-experiments.lisp
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;;
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(experiment
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positive
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(a b d)

‎network-debugger/presentation/demo-false-negative.lisp

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;; biohacker/trunk/network-debugger/presentation/demo-false-negative.lisp
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(experiment
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false-negative
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(a b)

‎network-debugger/presentation/demo-false-positive.lisp

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;;biohacker/trunk/network-debugger/presentation/demo-false-positive.lisp
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(experiment
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false-positive
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(a b f)

‎network-debugger/presentation/demo-negative.lisp

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;; biohacker/trunk/network-debugger/presentation/demo-negative.lisp
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(experiment
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negative
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(a)

‎network-debugger/presentation/demo-network.lisp

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;; biohacker/trunk/network-debugger/presentation/demo-network.lisp
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(network-debugger demo :debugging t :abducting t :rules :extended-reactions)
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(reaction r1 :reactants (c g) :products (a b) :enzymes (e1))

‎network-debugger/presentation/demo-positive.lisp

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;;biohacker/trunk/network-debugger/presentation/demo-positive.lisp
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(experiment
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positive
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(a b d)

‎network-debugger/stats.txt

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stats.txt
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new system (network-debugger) with new data (ecoli):
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* 1764 / 9854 rules run before experiment
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* 1799 / 9819 rules run for closing network

‎network-debugger/tests/pathways.lisp

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;; biohacker/trunk/network-debugger/tests/pathways.lisp
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(network-debugger simple :debugging t :rules :just-pathways)
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;; Network

‎network-debugger/tests/reversible.lisp

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;; biohacker/trunk/network-debugger/tests/reversible.lisp
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(network-debugger reversible :debugging t :rules :extended-reactions)
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;; Network

‎network-debugger/tests/simple.lisp

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(network-debugger simple :debugging t :abducting t)
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(network-debugger simple :debugging t :abducting t :log "~/src/lisp/biohacker/trunk/network-debugger/tests/simple-stats.log" )
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;; Network
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(reaction

‎network-debugger/tests/unknown-enzyme.lisp

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;; biohacker/trunk/network-debugger/tests/unknown-enzyme.lisp
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(network-debugger unknown-enzyme :debugging t :growth-patterns ((reaction-enabled ?r) (nutrient ?c) (enzyme-present ?e)) :abducting t)
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;; Network

‎network-debugger/tests/unknown.lisp

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;; biohacker/trunk/network-debugger/tests/unknown.lisp
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(network-debugger unknown :debugging t :rules :extended-reactions)
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;; Network

‎network-debugger/utils.lisp

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;; biohacker/trunk/network-debugger/utils.lisp
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(defun list-of (name els)
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(mapcar
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#'(lambda (el)

‎ptools/export-rxns.lisp

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;; biohacker/trunk/ptools/export-rxns.lisp
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(in-package :ecocyc)
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‎ptools/parse-biolog.py

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#biohacker/trunk/ptools/parse-biolog.py
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import sys
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class Biolog_parser:
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def __init__( self ):

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