the nih - nigms - sponsored protein structural initiative ( 1 ) initially sponsored seven pilot projects in structural genomics , including the southeast collaboratory for structural genomics ( secsg ) ( 2 ) . the structural genomics of caenorhabditis elegans ( sgce ) project established a pipeline for high - throughput protein expression , microarray crystallization screening , x - ray data collection and user - friendly bioinformatics . the initial sgce focus was the nematode worm c.elegans , one of the best - studied multicellular model organisms ( 3 ) whose complete genomic sequence is known ( 4 ) . the sgce project is facilitated by the c.elegans orfeome project ( 5 ) , which aims at cloning all predicted protein - encoding open reading frames ( orfs ) as gateway entry clones ( 6 ) . the 96-well plates of cdna supplied enabled a high - throughput approach to recombinant protein expression and analysis . however , a pipeline to express , purify and crystallize over 10  000 c.elegans orfs ( 7 ) required more comprehensive tracking for meaningful analysis . additional requirements for the project included sample tracking and monitoring group progress for a smooth transition between the expression , purification and crystallization groups . plates of cdna orfs for robotic screening needed to be prioritized based on the expectation of results . in order to prioritize , established external databases and analysis algorithms must be applied on a genome - wide basis . finally , the methods used to accomplish each step were updated on a regular basis ; therefore , the database and interface system needed to be flexible enough to rearrange and modify experiments before the data stored became obsolete with respect to the experiments performed . the resulting sgcedb is a database and interface framework that has been applied to a variety of genomes and heterogeneous experiment methodologies . the target i d used for selecting a single protein is generally the wormbase ( 8)  aceid , familiar to c.elegans researchers . unlike wormbase , which concentrates on genomic information , the sgcedb concentrates on information of the putative proteins . the sgce was among the first structural genomics groups to make its protein production data publicly available . the most detailed way of browsing the sgcedb is by viewing one of the 16  566 c.elegans individual proteins . in this view links are provided to wormbase website ( 10 ) , the orfeome project ( 5 ) and the protein information resource ( 11 ) if available . blast ( 12 ) results against the protein data bank ( pdb ) structures ( 13 ) are updated weekly . blast results against the non - redundant database ( 14 ) and pfam ( 15 ) results are periodically updated . theoretical values , such as isoelectric point and hydrophobicity , are calculated from the expasy site ( 16 ) . transmembrane protein ( 17 ) , signal peptide ( 18 ) and prosite ( 19 ) results are available . for each of the 11  727 proteins with experiments an example web page of a protein view with a completed structure ( 20 ) is shown in figure 1 . the xml reports are updated weekly and are intended to provide improved interoperability with external databases . database queries are used to format all results according to the targetdb and the protein expression , purification and crystallization ( pepcdb ) xml standards for structural genomics maintained at the pdb ( 13 ) . individuals interested in detailed results of a specific step can go directly to that page , e.g. structures. the modeling page contains secondary structures and other predictions available from proteinpredict ( 21 ) . the modeling page also provides distributions per plate and histograms over the entire database for calculated protein parameters . the parameter distribution per plate is used internally to prioritize efforts . a variety of per plate experimental reports are also available . the complete system was developed in close collaboration with the sgce project scientists and technicians . the infrastructure was constructed entirely with open - source tools including the apache web server , the python language and the postgresql database system . a more detailed summary of the design and data entry including figures is provided in supplementary data . the database of sgcedb is separated into two distinct parts : protein source and experiment tracking . each schema implements advanced database methods to efficiently and comprehensively track proteins , results and analyses throughout the experimental process . when a protein source is initially received or considered for study , the sequences are organized into plates and wells . the protein source schema has configurable plate geometry allowing it to track protein production , 96-well solubility screens and 384-well crystallization trials . by keeping plates , wells and sequences separate in the protein source schema data attributes can be assigned at an appropriate level . for instance , the pfam ( 15 ) algorithm is initially executed and stored once per sequence . experiment parameters common to an entire screening plate are stored once per plate whereas individual experiment results are stored at the plate level . this design provides efficient queries of experimental data by eliminating duplicate information and allowing the design to scale to experiments over the entire c.elegans genome . experiment history is stored in a condensed form , called parenthetical tree notation ( 22 ) . this notation is exceptionally useful for querying lineage information . populating the history tree is handled by the database during data entry , with the scientists only having to indicate a major benefit of storing an experiment history tree is the ability to efficiently retrieve every experiment that has influenced an experiment of interest . generic experiment table when tracking the sequence of experiments . by tracking experiment history using a generic experiment i d any combination of available experiments can be combined and tracked without a major database re - design . in general the sequence of experiments is fixed by protocol . however , in the event of an unexpected result , quality control experiments such as mass spectrometry and additional chromatography column experiments may be inserted anywhere in the sequence of experiments . all subsequent experiments will include the unplanned mass spectrometry in a query of its history . a benefit of zope is the ability to reuse common data entry components to quickly assemble entry forms for the bench scientist . the target i d used for selecting a single protein is generally the wormbase ( 8)  aceid , familiar to c.elegans researchers . unlike wormbase , which concentrates on genomic information , the sgcedb concentrates on information of the putative proteins . the sgce was among the first structural genomics groups to make its protein production data publicly available . the most detailed way of browsing the sgcedb is by viewing one of the 16  566 c.elegans individual proteins . in this view links are provided to wormbase website ( 10 ) , the orfeome project ( 5 ) and the protein information resource ( 11 ) if available . blast ( 12 ) results against the protein data bank ( pdb ) structures ( 13 ) are updated weekly . blast results against the non - redundant database ( 14 ) and pfam ( 15 ) results are periodically updated . theoretical values , such as isoelectric point and hydrophobicity , are calculated from the expasy site ( 16 ) . transmembrane protein ( 17 ) , signal peptide ( 18 ) and prosite ( 19 ) results are available . for each of the 11  727 proteins with experiments an example web page of a protein view with a completed structure ( 20 ) is shown in figure 1 . the xml reports are updated weekly and are intended to provide improved interoperability with external databases . database queries are used to format all results according to the targetdb and the protein expression , purification and crystallization ( pepcdb ) xml standards for structural genomics maintained at the pdb ( 13 ) . individuals interested in detailed results of a specific step can go directly to that page , e.g. structures. the modeling page contains secondary structures and other predictions available from proteinpredict ( 21 ) . the modeling page also provides distributions per plate and histograms over the entire database for calculated protein parameters . the parameter distribution per plate is used internally to prioritize efforts . a variety of per plate experimental reports are also available . the complete system was developed in close collaboration with the sgce project scientists and technicians . the infrastructure was constructed entirely with open - source tools including the apache web server , the python language and the postgresql database system . a more detailed summary of the design and data entry including figures is provided in supplementary data . the database of sgcedb is separated into two distinct parts : protein source and experiment tracking . each schema implements advanced database methods to efficiently and comprehensively track proteins , results and analyses throughout the experimental process . when a protein source is initially received or considered for study , the sequences are organized into plates and wells . the protein source schema has configurable plate geometry allowing it to track protein production , 96-well solubility screens and 384-well crystallization trials . by keeping plates , wells and sequences separate in the protein source schema data attributes can be assigned at an appropriate level . for instance , the pfam ( 15 ) algorithm is initially executed and stored once per sequence . experiment parameters common to an entire screening plate are stored once per plate whereas individual experiment results are stored at the plate level . this design provides efficient queries of experimental data by eliminating duplicate information and allowing the design to scale to experiments over the entire c.elegans genome . experiment history is stored in a condensed form , called parenthetical tree notation ( 22 ) . this notation is exceptionally useful for querying lineage information . populating the history tree is handled by the database during data entry , with the scientists only having to indicate a major benefit of storing an experiment history tree is the ability to efficiently retrieve every experiment that has influenced an experiment of interest . generic experiment table when tracking the sequence of experiments . by tracking experiment history using a generic experiment i d any combination of available experiments can be combined and tracked without a major database re - design . in general the sequence of experiments is fixed by protocol . however , in the event of an unexpected result , quality control experiments such as mass spectrometry and additional chromatography column experiments may be inserted anywhere in the sequence of experiments . all subsequent experiments will include the unplanned mass spectrometry in a query of its history . a benefit of zope is the ability to reuse common data entry components to quickly assemble entry forms for the bench scientist . currently the sgcedb framework has the capability to handle individual and plate - based experiments with external database reference and algorithm analysis . an experiment creation tool would generate table definitions , entry forms and standard html views based on data types specified in a graphical interface . the modular visualization methods would utilize java display layers to allow the user to superimpose additional information where it is most useful  for instance , secondary structure under the sequence and information content over a 3d structure ( 24 ) or gel markers by a gel image . the left - hand side shows the information available for all targets . the right - hand side shows the experimental data generated .
the sgcedb ( ) database / interface serves the primary purpose of reporting progress of the structural genomics of caenorhabditis elegans project at the university of alabama at birmingham . 
 it stores and analyzes results of experiments ranging from solubility screening arrays to individual protein purification and structure solution . external databases and algorithms 
 are referenced and evaluated for target selection in the human , c.elegans and pneumocystis carinii genomes . the flexible and reusable design permits 
 tracking of standard and custom experiment types in a scientist - defined sequence . 
 the database coordinates efforts between collaborators and is adaptable to a wide range of biological applications .