Hello Mark,

Thanks for this great extension, it came at the very right moment for our website.
I just switched to the new version of the package,  and it seems i have a little bug : the authors are not displayed on the front page anymore. Any idea what could be the reason?

Best regards,
marie

Hello Mark,
i think i have the same or nearly the same problem as Marie. I imported the bib-tex-file with articles from medline (medicine database). Here one article as an example:

@article{
   Author = {Aghazadeh, B. and Zhu, K. and Kubiseski, T. J. and Liu, G. A. and Pawson, T. and Zheng, Y. and Rosen, M. K.},
   Title = {Structure and mutagenesis of the Dbl homology domain},
   Journal = {Nat Struct Biol},
   Volume = {5},
   Number = {12},
   Pages = {1098-107},
   Abstract = {Guanine nucleotide exchange factors in the Dbl family activate Rho GTPases by accelerating dissociation of bound GDP, promoting acquisition of the GTP-bound state. Dbl proteins possess a approximately 200 residue catalytic Dbl-homology (DH) domain, that is arranged in tandem with a C-terminal pleckstrin homology (PH) domain in nearly all cases. Here we report the solution structure of the DH domain of human PAK-interacting exchange protein (betaPIX). The domain is composed of 11 alpha-helices that form a flattened, elongated bundle. The structure explains a large body of mutagenesis data, which, along with sequence comparisons, identify the GTPase interaction site as a surface formed by three conserved helices near the center of one face of the domain. Proximity of the site to the DH C-terminus suggests a means by which PH-ligand interactions may be coupled to DH-GTPase interactions to regulate signaling through the Dbl proteins in vivo.},
   Keywords = {Amino Acid Sequence
Blood Proteins/ chemistry/genetics
Caenorhabditis elegans Proteins
Catalytic Domain/ genetics
Cell Cycle Proteins/genetics/metabolism
Enzyme Activation
Escherichia coli
Frameshift Mutation
GTP Phosphohydrolases/genetics/ metabolism
GTP-Binding Proteins/genetics/metabolism
Guanine Nucleotide Exchange Factors
Guanosine Diphosphate/metabolism
Helminth Proteins/genetics/metabolism
Humans
Magnetic Resonance Spectroscopy
Models, Molecular
Molecular Sequence Data
Mutagenesis, Site-Directed
Nerve Tissue Proteins/genetics/metabolism
Phosphoproteins
Proteins/genetics/metabolism
Proto-Oncogene Proteins/ chemistry/genetics
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.
Sequence Alignment
Sequence Homology, Amino Acid
cdc42 GTP-Binding Protein
rhoA GTP-Binding Protein},
   Year = {1998} }

After the import nearly all is correctly displayed exapt the authors (it's empty):
 #            Authors      Title      Year      URLs      Category
 1                  Structure and mutagenesis of the Dbl homology domain       1998           default

If I open "Edit the reference" and leave it with "save", this error message is shown:

DB function failed with error number 1054Unbekanntes Tabellenfeld 'author' in field list. SQL=update aas_bib set author='Array',title='Structure and mutagenesis of the Dbl homology domain',journal='Na

I read that the new My SQL database has a different command structure or something like that:
http://www.vbulletin.com/forum/showthread.php?t=165325
but don't know what to do.

Can you please help me?

Best regards,
Jonas

P.S.: Your tool is really cool!!!

I have found the source of the problem.  References are assumed to be in the form:

@article{citationreference,
author={author name},
.
.
.
}

If the citation reference is missing then the parser I use fails.  I will see if I can fix this, but for now, the fix would be to change your bibtex string to :

@article{Aghaz98,
   Author = {Aghazadeh, B. and Zhu, K. and Kubiseski, T. J. and Liu, G. A. and Pawson, T. and Zheng, Y. and Rosen, M. K.},
   Title = {Structure and mutagenesis of the Dbl homology domain},
   Journal = {Nat Struct Biol},
   Volume = {5},
   Number = {12},
   Pages = {1098-107},
   Abstract = {Guanine nucleotide exchange factors in the Dbl family activate Rho GTPases by accelerating dissociation of bound GDP, promoting acquisition of the GTP-bound state. Dbl proteins possess a approximately 200 residue catalytic Dbl-homology (DH) domain, that is arranged in tandem with a C-terminal pleckstrin homology (PH) domain in nearly all cases. Here we report the solution structure of the DH domain of human PAK-interacting exchange protein (betaPIX). The domain is composed of 11 alpha-helices that form a flattened, elongated bundle. The structure explains a large body of mutagenesis data, which, along with sequence comparisons, identify the GTPase interaction site as a surface formed by three conserved helices near the center of one face of the domain. Proximity of the site to the DH C-terminus suggests a means by which PH-ligand interactions may be coupled to DH-GTPase interactions to regulate signaling through the Dbl proteins in vivo.},
   Keywords = {Amino Acid Sequence
Blood Proteins/ chemistry/genetics
Caenorhabditis elegans Proteins
Catalytic Domain/ genetics
Cell Cycle Proteins/genetics/metabolism
Enzyme Activation
Escherichia coli
Frameshift Mutation
GTP Phosphohydrolases/genetics/ metabolism
GTP-Binding Proteins/genetics/metabolism
Guanine Nucleotide Exchange Factors
Guanosine Diphosphate/metabolism
Helminth Proteins/genetics/metabolism
Humans
Magnetic Resonance Spectroscopy
Models, Molecular
Molecular Sequence Data
Mutagenesis, Site-Directed
Nerve Tissue Proteins/genetics/metabolism
Phosphoproteins
Proteins/genetics/metabolism
Proto-Oncogene Proteins/ chemistry/genetics
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, P.H.S.
Sequence Alignment
Sequence Homology, Amino Acid
cdc42 GTP-Binding Protein
rhoA GTP-Binding Protein},
   Year = {1998} }

Hi Mark,
the thing with the author works fine, thanks!!!

 B. Aghazadeh et al.       Structure and mutagenesis of the Dbl homology domain       Nat Struct Biol      1998      article

But is this format in the reference detail correct?
 Reference Details
Aghazadeh, B., Zhu, K., Kubiseski, T. J., Liu, G. A., Pawson, T., Zheng, Y. and Rosen, M. K. (1998), "Structure and mutagenesis of the Dbl homology domain", Nat Struct Biol, 5, 12: 1098-107.Abstract:Guanine nucleotide exchange factors in the Dbl family activate Rho GTPases by accelerating dissociation of bound GDP, promoting acquisition of the GTP-bound state. Dbl proteins possess a approximately 200 residue catalytic Dbl-homology (DH) domain, that is arranged in tandem with a C-terminal pleckstrin homology (PH) domain in nearly all cases. Here we report the solution structure of the DH domain of human PAK-interacting exchange protein (betaPIX). The domain is composed of 11 alpha-helices that form a flattened, elongated bundle. The structure explains a large body of mutagenesis data, which, along with sequence comparisons, identify the GTPase interaction site as a surface formed by three conserved helices near the center of one face of the domain. Proximity of the site to the DH C-terminus suggests a means by which PH-ligand interactions may be coupled to DH-GTPase interactions to regulate signaling through the Dbl proteins in vivo.Keywords:Amino Acid Sequence Blood Proteins/ chemistry/genetics Caenorhabditis elegans Proteins Catalytic Domain/ genetics Cell Cycle Proteins/genetics/metabolism Enzyme Activation Escherichia coli Frameshift Mutation GTP Phosphohydrolases/genetics/ metabolism GTP-Binding Proteins/genetics/metabolism Guanine Nucleotide Exchange Factors Guanosine Diphosphate/metabolism Helminth Proteins/genetics/metabolism Humans Magnetic Resonance Spectroscopy Models, Molecular Molecular Sequence Data Mutagenesis, Site-Directed Nerve Tissue Proteins/genetics/metabolism Phosphoproteins Proteins/genetics/metabolism Proto-Oncogene Proteins/ chemistry/genetics Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Sequence Alignment Sequence Homology, Amino Acid cdc42 GTP-Binding Protein rhoA GTP-Binding Protein

The picture in your documentation was different- it seems that the format doesn't work well.
What do you think? Was it in your frontend correct?

Best regard,
Jonas

I think that I may have found the source of this error.  I had </br> rather than <br /> for my linebreaks, which did not cause a problem in internet explorer but does cause a problem in other browsers, Firefox included.  I will fix the typo in the next release, coming soon.  If you want to fix the code yourself now, change lines 344-371 of jombib.html.php from:

      if ($row['abstract']!=""){
         echo "</br>";
         echo "</br>";
         echo "<b>Abstract:</b>";
         echo "</br>";
         echo $row['abstract'];
      }   
      if ($row['keywords']!=""){
         echo "</br>";
         echo "</br>";
         echo "<b>Keywords:</b>";
         echo "</br>";
         echo $row['keywords'];
      }   
      if ($row['note']!=""){
         echo "</br>";
         echo "</br>";
         echo "<b>Notes:</b>";
         echo "</br>";
         echo $row['note'];
      }
      if ($row['annote']!=""){
         echo "</br>";
         echo "</br>";
         echo "<b>Annotations:</b>";
         echo "</br>";
         echo $row['annote'];
      }

to:

      if ($row['abstract']!=""){
         echo "<br />";
         echo "<br />";
         echo "<b>Abstract:</b>";
         echo "<br />";
         echo $row['abstract'];
      }   
      if ($row['keywords']!=""){
         echo "<br />";
         echo "<br />";
         echo "<b>Keywords:</b>";
         echo "<br />";
         echo $row['keywords'];
      }   
      if ($row['note']!=""){
         echo "<br />";
         echo "<br />";
         echo "<b>Notes:</b>";
         echo "<br />";
         echo $row['note'];
      }
      if ($row['annote']!=""){
         echo "<br />";
         echo "<br />";
         echo "<b>Annotations:</b>";
         echo "<br />";
         echo $row['annote'];
      }