Kenneth,

The data you ask about are available, with much more, in the bulk
flybase gene data files, from ftp://flybase.bio.indiana.edu/flybase-data/ 
(see http://flybase.bio.indiana.edu/.data/docs/refman/refman-D.html
D.2.2. Bulk data in ACODE and XML formats for some basic info on these).
The full flat files (~ 100 MB in size) with these data 
key=value format at
  ftp://flybase.bio.indiana.edu/flybase-data/acode/data/FBgn.acode
xml format at
  ftp://flybase.bio.indiana.edu/flybase-data/xml/FBgn.xml


There are also some other ways to get the particular (a), (b) and (c)
requests of yours.  

For both (a and c) list all Dmel. genes, and  a file of all  homologues  
Use the gene search form
  http://flybase.bio.indiana.edu/genes/fbgquery.hform
with Species field set to Dmel, no other entries, and get

Query:   [libs={FBgn PFgn}-org:Dmel] but not [libs-cla:uncertain],  No. matches= 40626 

If you want a summary table without homolog fields, 
find "Page to item" box below list, enter
[ 1] and [999999] items, select Format: spreadsheet, tabbed, and get this
# FlyBase Genes query results. Query: [libs={FBgn PFgn}-org:Dmel] <i>but not</i> [libs-cla:uncertain], No. matches= 40626
# # Symbol  Name  Map Alleles Stocks  Refs  DNA acc.  Date  Rept. size  ID
1 alphagamma-element  alphagamma element  87C1  2 - 10  3 23 Aug 02 3300  FBgn0004084
2 beta'Cop  beta'-coatomer protein  34B4  1 - 9 15  23 Aug 02 3258  FBgn0025724
3 beta'Cop  - 34B9  - - - - 24 Oct 02 166 PFgn0025724
...
40623 zwilch  - 100B3 - - - - 24 Oct 02 162 PFgn0061476
40624 Zwim  Zwirbelmuetze - 1 - 1 - 22 Aug 02 833 FBgn0062246
40625 Zyx102EF  - 102E--F 1 - 10  6 22 Aug 02 2369  FBgn0011642
40626 Zyx102EF  - - - - 1 - 24 Oct 02 170 PFgn0011642

To get the Homolog field along with others, find below this
  Batch Download 
and select these or other fields, where HG is the homology field
 Report only Select fields:ID,GSYM,NAM,HG

Set Format to Spreadsheet, tabbed
Set Fetch items to All (maybe test first with a few hundred to see if
it is what you want). 

You will get this kind of table
FlyBase_ID  Symbol  Full_name Similar_genes
FBgn0010339 128up upstream of RpIII128  ; Caenorhabditis elegans C02F5.3  WP:CE00039; Homo sapiens 'neural precursor cell expressed, developmentally down-regulated 3'  gi:4758796; Mus musculus Nedd3  MGI:97296; Saccharomyces cerevisiae 'HYPOTHETICAL 40.7 KD PROTEIN IN PYK1-SNC1 INTERGENIC REGION'  SWP:P39729 gi:731276; Xenopus laevis 'DEVELOPMENTALLY REGULATED GTP-BINDING PROTEIN DRG (XDRG)'  SWP:P43690 gi:1169421; 
FBgn0005673 1360  1360 element  
FBgn0020238 14-3-3epsilon   
FBgn0004907 14-3-3zeta    ; Caenorhabditis elegans F52D10.3  WP:CE03389; Homo sapiens 'tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide'  gi:4507953; Mus musculus Ywhaz  MGI:109484; Saccharomyces cerevisiae BMH2  SGDID:L0000186; rat '14-3-3 protein isoform zeta'  PIR:JC5232 gi:2143553; 


For (b), gene interaction data is complex and currently we don't
have a summarized table option. It is something we are working
on.  This includes 6 data fields:
Interacts genetically with  [WTI]
Genetic interaction (effect, class)  [GIC]
Genetic interaction (class, effect)  [GIC2]
Genetic interaction (effect, anatomy) [GIA]
Genetic interaction (anatomy, effect) [GIA2]
Genetic interaction info.   [GII]

GIC,GIA.. here are the keys for these fields in flybase data.
This is fairly complex data, and currently the flybase web interface
doesn't have a batch download option to select just this data.
You can obtain the full flybase data set which includes this,
in XML or simpler tag=value formats, and parse out with software the 
gene interaction fields. 

Gene interaction data fields are attributed to particular experimental
references for  individual alleles of a given gene record.
Within the flybase gene record they appear as
 Gene a
   allele a[1]
     reference R1
       GIC, GIC2, ... fields
     ref. R2 
        GIC, ...
    allele a[2]
     ...

I've appended at end an experimental perl script for parsing
out gene interaction data from flybase FBgn.acode bulk data,
producing graph structure data.


-- Don Gilbert

#!/usr/local/bin/perl
# fbgiparse.pl

=head1 NAME

fbgiparse - flybase gene iteraction data parser
  
=head1 NOTES

parse gene interaction fields from flybase gene data FBgn.acode
  ftp://flybase.bio.indiana.edu/flybase-data/acode/data/FBgn.acode
write as digraph or related graph data

This includes 6 data fields:
Interacts genetically with  [WTI]
Genetic interaction (effect, class)  [GIC]
Genetic interaction (class, effect)  [GIC2]
Genetic interaction (effect, anatomy) [GIA]
Genetic interaction (anatomy, effect) [GIA2]
Genetic interaction info.   [GII]

GIC,GIA.. here are the keys for these fields in flybase data.
This is fairly complex data, and currently the flybase web interface
doesn't have a batch download option to select just this data.
You can obtain the full flybase data set which includes this,
in XML or simpler tag=value formats, and parse out with software the 
gene interaction fields. 

Gene interaction data fields are attributed to particular experimental
references for  individual alleles of a given gene record.
Within the flybase gene record they appear as
 Gene a
   allele a[1]
     reference R1
       GIC, GIC2, ... fields
     ref. R2 
        GIC, ...
    allele a[2]
     ...
   

This is experimental software; Don Gilbert, gilbertd@bio.indiana.edu, 2002

=cut

use lib('/Users/gilbertd/perl','/bio/perlib');

use strict;
use vars qw( $nodenums %didnode %nodenam %regex);

#use Graph;
#use Graph::Directed;
#use Graph::Writer::Dot;

#=head2 notes
#
# graphviz dot graphs: 
#  foreach f ( $gi )
#   set w=`fgrep -c 'label=' $f`
#   if ($w > 2) then
#    $gr/bin/dot -Tgif -Nshape=box -Nfontsize=8 -o$f.gif $f >& /dev/null
#   endif
#  end
#
#  $gr/bin/dot -Tgif -Nshape=box -Nfixedsize=true -Nwidth=0.1 -Nstyle=invis \
#   -Gsize="15,7" -Grotate=90 -Gratio=compress -o$f.gif $f > & /dev/null
#  
#=cut

my $DG;
my @keys= qw(GIA GIA2 GIC2 GIC WTI);
my %keys= map{ $_,1; }@keys;

my $path;
#$path= '/Volumes/MacHome/bio/flybase/geneinter/';
#$path= '/Users/gilbertd/bio/flybase/fbjava/fbrj/fbobs/';
$path= './';

my $file;
# $file= "dally.acode";  
$file= "FBgn.acode";  

chomp($path);
my $savep= 'gi';

my $f= (@ARGV) ? shift @ARGV  : "$path/$file";
open(F,$f) or die $f;

init();

my $testline= 0; ##1;
my $dographviz= 1;
my $dograph= 0;
my $testlimit= 0;
my $showprogress= 0; #1;
my $dogene= ''; # 'dally';
my %syms= (); my %rete= (); my @rete= (); my %eg= ();
my $mainsym; my $mainid;
my $atkey;

$savep= $dogene if ($dogene && $dogene ne 'nogene');

graphtop();

my $nrec= 0;
my $indogene= 0;
while(<F>){
  chomp;
  if (/^GENR/) { startrec(); }
  elsif (/^RETE\|(.+)/) {
    @rete= split "\t", $1;
    %rete= map{ split(/\s/,$_,2); } @rete;
    $mainsym= $rete{GSYM}; $mainsym =~ s/^\s*\d\s+//;
    $mainid= $rete{ID}; $mainid =~ s/^\s*\d\s+//;
    if ($testline && $mainsym =~ /$dogene/) {
      print STDERR "# at $mainsym: $_\n";
      $indogene= 1;
      }
    else { $indogene= 0; }
    # print "# node  [name=\"$mainsym\" id=$mainid ];\n" if $testline;
    }
  elsif (/^# EOR/) { 
    endrec(); 
    last if ($testlimit && $nrec>=$testlimit); 
    }
  elsif (/^(\w+)\|(.+)/) {
    my ($k,$v)= ($1,$2); 
    if ($keys{$k}) { $atkey= $k; edge($atkey,$v); }
    else { $atkey= 0; }
    }
  elsif ($atkey && /^\|(.+)/) {
    edge($atkey,$1);  
    }
}

graphend();

sub graphtop {
# if ($dograph){
#   $DG= new Graph::Directed;
#   }
  if($dographviz){
    print "digraph geneinter ";
    ## if ($title) { print "[label=\"$title\"]"; }
    print "{\n";
    ## add graph styles node [fontname=helvetica,fontsize=10];
    ## page="8.5,100" ; ratio=???? ; ...
    }
}

sub graphend {
  print "\n}\n" if($dographviz);
  
# if ($dograph) {
#   #  @S = $DG->strongly_connected_components;
#   
##    my $outh= IO::Handle->new_from_fd( fileno(STDOUT),"w"); # *STDOUT;
#     my $writer = Graph::Writer::Dot->new();
#   my $outh;
#   
##    $outh = IO::File->new(">$path/gi2.dot");
##    warn "Write to $path/*.dot\n";
##    open(DOT,">gi2.dot") || die "'gi2.dot'";
##    $outh= *DOT;
#       
#   my $fn;
#   $fn= "$path/$savep-plain.dot";
#   warn "$fn\n";
#     my $T = $DG;
#   $T->set_attribute('name','geneinter');
#    $writer->write_graph($T, $fn);
#
#   $fn= "$path/$savep-strong.dot";
#   warn "$fn\n";
#     $T = $DG->strongly_connected_graph;
#   $T->set_attribute('name','strongly_connected_graph');
#    $writer->write_graph($T, $fn);
#   
#   $fn= "$path/$savep-MST_Kruskal.dot";
#   warn "$fn\n";
#   $T = $DG->MST_Kruskal;
#   $T->set_attribute('name','MST_Kruskal');
#    $writer->write_graph($T, $fn);
#
#   my $node= nodenum($dogene);
#   if ($node) {
#     $fn= "$path/$savep-MST_Prim.dot";
#   warn "$fn\n";
#     $T = $DG->MST_Prim($node);
#     $T->set_attribute('name','MST_Prim');
#     $writer->write_graph($T, $fn);
#   
#   ## no good, memory  pig
##      warn "$path/gi-Dijkstra.dot\n";
##      $T = $DG->SSSP_Dijkstra($node);
##      $T->set_attribute('name','Dijkstra');
##      $writer->write_graph($T, "$path/gi-Dijkstra.dot");
#     }
#   
##    warn "$path/gi-APSP.dot\n";
##    $T = $DG->APSP_Floyd_Warshall;
##    $T->set_attribute('name','APSP_Floyd_Warshall');
##   $writer->write_graph($T, "$path/gi-APSP.dot");
#
##   $T = $G->TransitiveClosure_Floyd_Warshall;
#
#
##    $T = $DG->SSSP_DAG($s);
##    $T->set_attribute('name','SSSP_DAG');
##    $writer->write_graph($T, $outh);
#
#   close($outh) if (ref $outh);
#   }
}

sub edge {
  my($k,$v)= @_;
  my $kind= '?';
  
  if ($k eq 'WTI') {
    $v =~ s/\s.+$//;
    $syms{$v}++;
    }
  else {
    # print "$k: $v\n" if $testline;
    
    my $showit= ($testline && (/$dogene/ || $testlimit));
    
    my @m= m/$regex{regenes}/g; 
    print "# syms: ",join(",",@m)," =  " if ($showit);
    
    my $re;
    $re= $regex{reNonint};
    if ($v =~ m/$re/) {
      $kind= 'reNonint';
      showre('reNonint',$re,$v) if ($showit);
      }
    elsif ($v =~ m/$regex{reInter}/) {
      foreach my $r (qw(reSupper reSuppby reEnher reEnhby)) {
        $re= $regex{$r};
        if ($v =~ m/$re/) {
          $kind= $r;
          showre($r,$re,$v) if ($showit); 
          last;
          }
        }
      }
    else {
      $kind= 'unknown';
      showre('unknown','.',$v) if ($showit);
      }

    for my $m (@m) {
      next if ($m eq 'Scer\GAL4'); # ~= /Scer|GAL4/);
      $eg{$m}{$kind}++;
      }

    print "\n" if ($showit);
    }
}

sub showre {
  my $r= shift;
  my $re= shift;
  my $vx= shift;
  $vx =~ s/($re)/\U$1/; $vx =~ s/\@.+$//;
  print " $r: $vx";
}
  
sub startrec {
  %syms= (); %rete= (); @rete= (); %eg= ();
  # print "\n";
}


sub nodenum {
  my ($m,$dosave,$id)= @_;
  my $nd= $didnode{$m};
  unless($nd) {
    ++$nodenums;
    $nd= 'n'.$nodenums;
    $didnode{$m}= $nd;
    $nodenam{$nd}= $m;
    if ($dosave && $dographviz) {
      print "$nd [label=\"$m\"";
      print " id=$id" if ($id);
      print "];\n";
      }
#   if ($dosave && $dograph) {
#     $DG->add_vertex($nd);
#     $DG->set_attribute('label', $nd, $m);
#     $DG->set_attribute('id', $nd, $id) if ($id);
#     }
    }
  return $nd;
}

sub endrec {
  # dump %syms, 
  if ($indogene) {
    print STDERR "# endrec $mainsym: ".join(",",keys %eg)."\n";
    }
  return unless(%eg);
  $nrec++;
  
  my $showit= ($testline && ($testlimit || ($mainsym =~ /$dogene/)));
  unless ($showit) {
    foreach my $m (keys %eg) { $showit=1 if ($m =~ /$dogene/); }
    }
 
  if ($showprogress) {
    print STDERR '.';
    print STDERR " $mainsym $nrec\n" if (($nrec % 50) == 0);
    }
  return unless(
    $testline ? $showit : $dograph||$dographviz 
    );
          
  my $nmain= nodenum( $mainsym,($testline ? $showit : $dographviz),$mainid);
  print "# node $nmain [name=\"$mainsym\" id=$mainid ];\n" if $showit;

  for my $m (sort keys %eg) {
    my $nm= nodenum($m, ($testline ? $showit : $dographviz));
    my $nam= $nodenam{$nm};
    for my $k (sort keys %{$eg{$m}}) {
      my $w= $eg{$m}{$k};
      $w= -$w if ($k =~ /Sup/);
      
#     if ($dograph) {
#          if ($k =~ /by$/) { $DG->add_weighted_edge($nm, $w, $nmain); }
#       elsif ($k =~ /er$/) { $DG->add_weighted_edge($nmain, $w, $nm); }
#       # else ($k =~ /unknown|reNonint/) { $DG->add_weighted_edge($mainsym, 0, $nam); }
#       }
        
      if($dographviz && !$testline) {
           if ($k =~ /by$/) { print "$nm -> $nmain [weight=$w];\n"; }
        elsif ($k =~ /er$/) { print "$nmain -> $nm [weight=$w];\n"; }
        elsif ($k =~ /unknown|reNonint/) { print "$nmain -- $nm [weight=$w];\n"; }
        }
        
      if($showit && !$dograph) {
        if ($k =~ /by$/) { print "${nm} -> ${nmain} [weight=$w k=$k];\n"; }
        if ($k =~ /er$/) { print "${nmain} -> ${nm} [weight=$w k=$k];\n"; }
        if ($k =~ /reNonint/) { print "${nmain} -- ${nm} [weight=$w k=$k];\n"; }
        if ($k =~ /unknown/) { print "${nmain} -- ${nm} [weight=$w k=$k];\n"; }
        }
      }
    }
  
    
  # print "\n# ------------------\n";
}

sub init {
%regex= (
  reNonint => 'non-(suppress|enhanc)',
  reInter => '\W*(suppress|enhanc)',
  reSupper => '\W*suppress(or|es)\W',
  reSuppby => '\W*suppress(ible)\W',
  reEnher => '\W*enhanc(er|es)\W',
  reEnhby => '\W*enhanc(eable)\W',
  # regenes => '\@([^@<]+)[@<]',
  regenes => '\@([^@<]+)[^@]*\@',
);

}

=head2 regex for GeneInter fields

  reNonint = new RE("non-(suppress|enhanc)");  
  reInter = new RE("\\W(suppress|enhanc)");  
  reSupper = new RE("\\W*suppress(or|es)\\W"); //.+(of)? //? non-suppressor
  reSuppby = new RE("\\W*suppress(ible)\\W");  //.+(by)?
  reEnher  = new RE("\\W*enhanc(er|es)\\W");  //.+(of)?
  reEnhby  = new RE("\\W*enhanc(eable)\\W");   //.+(by)?// what of non-enhanceable by
  reGenes  = new RE("@([^@<]+)[@<]");
  
  int ikind;
  if (reNonint.isMatch(s)) {
    ikind= kOtherInter;
    }
  else if (reInter.isMatch(s)) {
    if (reSupper.isMatch(s))  ikind= kSupper;
    else if (reSuppby.isMatch(s)) ikind= kSupby;
    else if (reEnher.isMatch(s))  ikind= kEnher;
    else if (reEnhby.isMatch(s))  ikind= kEnhby;
    else ikind= kOtherInter;
    }
  else { 
    ikind= kOtherInter;
    }   
  REMatchEnumeration ren= reGenes.getMatchEnumeration( s);
  while (ren.hasMoreMatches()) {
    rem= ren.nextMatch();
    String sym= rem.substituteInto("$1");
    interset[ikind].put(sym,sym); // count ?
    }

=cut