Log of updates to the Globin Gene Server

• 2003-Apr-1
  Added new GALA database

• 2001-Feb-9
  Added new HbVar database

• 1999-Nov-8
  New version of sim4 and blastlib.

• 1999-Oct-17
  Multi-pips of E. coli and selected enteric bacteria.

• 1999-Oct-4
  New version of sim4 and blastlib.

• 1999-Sep-12
  Two examples using Laj, our new interactive viewer for pairwise alignments.

• 1999-Aug-10
  Associated materials for the paper

  Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions

  are now available, plus source code.

• 1999-Jul-27
  New version of sim4 and blastlib (formerly simlib).

• 1999-Jul-8
  Updated HUGO links.

• 1999-Jul-6
  New PipMaker facility for creating percent identity plots.

• 1999-Mar-31
  Added link to:
  • Comprehensive Sickle Cell Centers -- Statistics and Data Management Center

• 1999-Mar-2
  Added links to:
  • Joint Center for Sickle Cell and Thalassemic Disorders
  • University of Massachusetts Chime Resources: Hemoglobin
  • Abstract of "Evolution of hemoglobin" paper

• 1999-Feb-25
  
  • Home page reorganized.
  • New essay about how the site supports functional genomics.
  • Updated list of publications.

• 1998-Dec-4
  Minor improvements to the WebGlimpse search page.

• 1998-Nov-25
  A WebGlimpse facility has been added that can search through the pages of 1) this entire site, or 2) just the Syllabi.

• 1998-Oct-12
  The alignment analysis pages under "Conserved regions in alignments" now allow the user a choice between our old and new multiple alignments of the beta-globin cluster.

• 1998-Sep-12
  The dbERGE query facilities (Genie, Tapestry, and Lamp Jr.) are working again.

• 1998-Aug-17
  Added a link for the SRS version of A Syllabus of Human Hemoglobin Variants (1996).
  Added an image depicting the composition of hemoglobin.

• 1998-Aug-9
  Interactive pairwise alignment diagrams added; E. coli vs. Salmonella removed.

• 1998-Jul-29
  Added link to APoGI.

• 1998-Jul-15
  The list of publications has been greatly expanded, complete with links to PubMed where applicable.

• 1998-Jul-14
  The simlib software is now available for download.

• 1998-Jul-8
  The contacts page has been updated, and ordering information for the Syllabi added.

• 1998-Jun-20
  Some of the Thalassemia Syllabus is now available.

• 1998-Jun-10
  Sample images (in .ps and .pdf formats) of multiple alignments of HSs in the beta LCR.

• 1998-May-21
  The sim4 software is now available for download.

• 1998-May-5
  The sim96 software submitted to SPEC is now available for download.

• 1998-May-2
  New utilities for locating various kinds of conserved regions in the multiple alignment.

• 1998-Apr-24
  Pairwise alignment of E. coli vs. Salmonella (clickable map).

• 1998-Apr-10
  Added pointers to several other sites, including two for aligning user-specified sequences.

• 1998-Feb-11
  Added data from two more papers to dbERGE (Lam96 and Elnitski97).

• 1997-Oct-30
  A few corrections to A Syllabus of Human Hemoglobin Variants (1996).

• 1997-Oct-20
  An on-line version of A Syllabus of Human Hemoglobin Variants (1996) is now available.

• 1997-Oct-14
  The pairwise alignment examples (pip diagrams) have been expanded.

• 1997-Jul-30
  Added pairwise alignment examples (pip diagrams).

• 1997-Jul-9
  Queries:
  
  • It's finally here! Our new Java interface, called Lamp Jr., makes it very easy to submit basic queries to the Database of Experimental Results.
  • A performance kludge in Genie's query engine produces a time savings of about 70% on a typical DNA_transfer_experiment query.
  Schema:
  
  • The schema uses a new keyword TEXT to help interface software to distinguish fields that are likely to contain long descriptions.
  • Origin choices are now listed explicitly, rather than depending on the not-yet-implemented FOREIGN_KEY feature.
  • Choices for many fields have been expanded or adjusted, including gene names, cell types, non_LCR_enhancers, mouse tissues, mouse ages, and induction.
  • The results section of the DNA_transfer_experiment table has been expanded to record percent_of_cells_expressing, expression_nature, integration_position, inducibility, chromosome expression levels, and copy_number.
  • The binding_assay table can now record multiple proteins for each regional_effect or gelshift complex.
  • A "strand" field has been added to the hypersensitive_site table.
  • Most of the non_beta_g_region fields are now optional, because their values are sometimes difficult to obtain.
  Data:
  
  • The Database of Experimental Results now contains 1416 records (or "tuples") from 47 papers.
  Diagrams:
  
  • A bug was fixed that affected the way the Tapestry drawing program calculates the "absolute" coordinates for a construct segment or protein binding region.

• 1996-Sep-26
  Minor clarifications to the query forms for drawing DNA transfer experiments and binding assays.

• 1996-Aug-11
  
  • A new, completely rewritten version of the alignment display tool (lat) has been installed.
  • The interface form for custom formatting and analysis of the alignment has been modified to conform with the new program, but it still does not provide the user with means to use some of the powerful new features of lat. However, all of the important old ones are still supported.

• 1996-Jul-1
  Schema:
  
  • The hypersensitive_site table has been expanded.
  • A new field for "mouse_line" has been added, along with more CHOICE_OF values for cell types, species and gene names, etc.
  • Preliminary schemas for the new hemoglobinopathy tables have been added, but no data is available online yet.
  Data:
  
  • 16 new papers have been added to the Database of Experimental Results, and more are on the way.
  Genie:
  
  • There is a new function CONTAINS for doing substring searches in text fields; please see Writing Genie queries for more details.
  • Punctuation is no longer ignored (because we sometimes need to distinguish between + and -, for example).
  • Genie can now handle comparisons and arithmetic that use mixtures of INTEGER and REAL numbers.
  • Output has been rearranged for better convenience: first the number of rows retrieved, then the data, and lastly the schema for it (which is used only by other programs).
  • There were some minor bug fixes, plus program reorganization for better API and modularity.
  • Speed--Genie runs faster than before, and there is also a new "daemon" helper program that sits listening for your queries (with the data already loaded) and passes them on to Genie for execution. This makes the queries run faster than they otherwise would. [However, you may notice that the queries seem slower than before, not faster; this is because there's a lot more data now. We need to work more on this...]
  Tapestry:
  
  • The Tapestry program, which draws the graphical representation of query results, has an improved layout and a new legend capability that gives more details about the displayed data.
  Glop:
  
  • A new documentation page has been written for Glop; please see Writing Glop queries. It is much easier to understand than before, but is still intended for users who already know the Prolog programming language. If you don't know Prolog, please use Genie instead.
  Links:
  
  • A new link was added, to EpoDB at the University of Pennsylvania's Computational Biology & Informatics Laboratory.

• 1995-Dec-12
  A major revision, including:
  
  • The database of experimental results now uses a new nested data model which allows sets, lists, and variants. This has required a complete overhaul of the database schema , plus revisions to all of the associated software and data files. (Please see the documents page for more information.)
  • More papers have been added to the database of experimental results.
  • The GlobinInfo program has been replaced by Glop, which allows more powerful queries based on the Prolog programming language.
  • Graphical representation of query results is now available for binding assays as well as for DNA transfer experiments.
  • The facilities for locating restriction enzyme cutting sites have been enhanced and expanded.
  • The query-by-forms facility and the filldata program are temporarily unavailable while they are being upgraded.

• 1995-Feb-13
  Minor modifications to the form for custom alignment formatting and its on-line help.

• 1994-Nov-15
  Schema changes:
  
  • A "species" field has been added to the "origin" table, so you can now select all experiments involving, say, rabbit constructs regardless of which rabbit origin was used.
  Query changes for Genie:
  
  • You can now write selection criteria that refer directly to the "origin", "start", and "stop" within a "location" field.
  • Error messages have been improved for certain kinds of syntax errors.

• 1994-Oct-28
  New features in the GlobinInfo query language:
  
  • One variable can now be used to access all attributes of a relation, and additional specifications can also refer to any of those attributes.
  • The command contains_match, which is similar to Genie's MATCHES command, has been implemented.
  • The command overlaps has been implemented.
  • The command member allows you to specify a set of acceptable values for a variable.

• 1994-Oct-6
  Syntax changes in schema and data languages:
  
  • Schemas now use SET_OF for entire relations in addition to sub-relations for consistency.
  • Data files now use BEGIN/END instead of ENTRY and ITEM
  • Semicolons are no longer used at the end of each line.
  Schema changes:
  
  • A new "units" table has been added with full descriptions for the "result_units" in the "DNA_transfer_experiment" table, as well as short unit classes for use as labels in illustrations. The tuples in "DNA_transfer_experiment" now specify the units with a code whose type is "FOREIGN_KEY units".
  • An optional "tuple" field has been added to "basic_table" so the GGS staff can assign identifying codes to each tuple for administrative purposes.
  • The "location" field is now OPTIONAL so it can be NULL for control runs.
  Query changes for Genie:
  
  • Functions for MATCHES, OVERLAPS, and EMPTY have been implemented, as well as RETRIEVE (var.ALL) to report all attributes from a relation without listing them explicitly in the query.
  • The output from SHOW SCHEMA and SHOW TUPLES is now presented in the same format required for input of schemas and data.
  Medline abstracts:
  
  • Medline abstracts are now listed for all published papers currently included in the database of experimental results.

• 1994-Sep-28
  New publications added to the documentation page.

• 1994-Sep-9
  Forms based alignment customization with user-defined motifs or automatic searching of the Transcription Factor Database is now available.

• 1994-Aug-22
  Carry-over feature removed:
  
  • The feature that previously allowed attribute values to "carry over" from one tuple to the next has been removed because it was too confusing. When submitting data, you must now explicitly list all the attribute values you intend for a tuple to have.
  Schema changes:
  
  • "Result" attributes in the "DNA_transfer_experiment" table are now handled via the SET_OF construction, similar to mutations.
  • The "binding_assay" and "DNA_transfer_experiment" tables have a new field for recording the orientation of an oligonucleotide/mutant relative to the original (5'->3') sequence.
  • The "reference" table has two new fields: "note" for clarifying terminology changes in titles, and "num" for journals that have both volumes and numbers.
  • There is a new field in "basic_table" (and therefore also in the "hypersensitive_site", "binding_assay", and "DNA_transfer_experiment" tables) to record further corrections or clarifications provided by the authors.
  Carriage returns:
  
  • The programs that read submitted data and queries have now been corrected to handle the carriage return characters (ASCII 13) that are inserted by many non-Unix computers.
  Non-optional attributes:
  
  • The program that reads in data now checks to make sure that all non-optional attributes do in fact have valid values.
  Minor improvements to the filldata program:
  
  • The output buffer is flushed after each tuple is saved, so no "saved" data is lost if the program ends prematurely.
  • The "quit" mechanism is less confusing.
  • The makefile has been corrected to work properly with Turbo C++.

• 1994-Aug-1
  A new standalone program called filldata provides a guided, interactive way to prepare experimental data for submission to the Globin Gene Server. C source code is available directly from the server or by ftp from globin.cse.psu.edu.

• 1994-Jul-14
  Schema changes:
  
  • Some attribute names have been changed in the "DNA_transfer_experiment" table.
  • The "caption" table has been removed; caption descriptions are now entered directly into the "DNA_transfer_experiment" table as "result1_units" and "result2_units".
  • The "contributor" attribute is no longer optional.
  • Correction to the "assay" list in the "binding_assay" table.
  • Improved descriptions were added for some tables and attributes.

• 1994-Jul-8
  A new version of laps works around a bug in some Level 2 PostScript printers.