Log of updates to the Globin Gene Server
Added new GALA database
Added new HbVar database
New version of sim4 and blastlib.
Multi-pips of E. coli and selected enteric bacteria.
New version of sim4 and blastlib.
Two examples using Laj, our new interactive viewer for pairwise alignments.
Associated materials for the paper
are now available, plus source code.
- Comparison of five methods for finding conserved sequences in multiple
alignments of gene regulatory regions
New version of sim4 and blastlib (formerly simlib).
Updated HUGO links.
New PipMaker facility for creating percent identity plots.
Added link to:
- Comprehensive Sickle Cell Centers -- Statistics and Data Management Center
Added links to:
- Joint Center for Sickle Cell and Thalassemic Disorders
- University of Massachusetts Chime Resources: Hemoglobin
- Abstract of "Evolution of hemoglobin" paper
- Home page reorganized.
- New essay about how the site supports functional genomics.
- Updated list of publications.
Minor improvements to the WebGlimpse search page.
A WebGlimpse facility has been added that can search through
the pages of 1) this entire site, or 2) just the Syllabi.
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.
The dbERGE query facilities (Genie, Tapestry, and Lamp Jr.)
are working again.
Added a link for the SRS version of A Syllabus of Human
Hemoglobin Variants (1996).
Added an image depicting the composition of hemoglobin.
Interactive pairwise alignment diagrams added;
E. coli vs. Salmonella removed.
Added link to APoGI.
The list of publications has been greatly expanded, complete with links to PubMed
The simlib software is now available for download.
The contacts page has been updated, and ordering information for the Syllabi added.
Some of the Thalassemia Syllabus is now available.
Sample images (in .ps and .pdf formats) of multiple alignments of HSs
in the beta LCR.
The sim4 software is now available for download.
The sim96 software submitted to SPEC is now available for download.
New utilities for locating various kinds of conserved regions in the
Pairwise alignment of E. coli vs. Salmonella (clickable map).
Added pointers to several other sites, including two for aligning
Added data from two more papers to dbERGE (Lam96 and Elnitski97).
A few corrections to A Syllabus of Human Hemoglobin Variants (1996).
An on-line version of A Syllabus of Human Hemoglobin Variants (1996)
is now available.
The pairwise alignment examples (pip diagrams) have been expanded.
Added pairwise alignment examples (pip diagrams).
- It's finally here! Our new Java interface, called Lamp Jr.,
makes it very easy to submit basic queries to the Database of
- A performance kludge in Genie's query engine produces a time savings
of about 70% on a typical DNA_transfer_experiment query.
- 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
- 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
- Most of the non_beta_g_region fields are now optional, because
their values are sometimes difficult to obtain.
- The Database of Experimental Results now contains
1416 records (or "tuples") from 47 papers.
- A bug was fixed that affected the way the Tapestry
drawing program calculates the "absolute"
coordinates for a construct segment or protein binding
Minor clarifications to the query forms for drawing DNA transfer
experiments and binding assays.
- 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.
- 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.
- 16 new papers have been added to the Database of
Experimental Results, and more are on the way.
- 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...]
- 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.
- A new documentation page has been written for Glop;
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
- A new link was added, to
EpoDB at the University of Pennsylvania's Computational
Biology & Informatics Laboratory.
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
, plus revisions to all of the associated software
and data files. (Please see the
page for more information.)
- More papers have been added to the database of experimental
- 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.
Minor modifications to the form for custom alignment formatting
and its on-line help.
Query changes for Genie:
- 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.
- 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
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.
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.
Query changes for Genie:
- 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
- An optional "tuple" field has been added to
"basic_table" so the GGS staff can assign
identifying codes to each tuple for administrative
- The "location" field is now OPTIONAL so it
can be NULL for control runs.
- 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
- Medline abstracts are now listed for all published papers
currently included in the database of experimental results.
New publications added to the documentation page.
Forms based alignment customization with user-defined motifs or
automatic searching of the Transcription Factor Database
is now available.
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.
- "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",
"DNA_transfer_experiment" tables) to record
further corrections or clarifications provided by the
- 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.
Minor improvements to the filldata program:
- The program that reads in data now checks to make sure that
all non-optional attributes do in fact have valid values.
- The output buffer is flushed after each tuple is saved, so
no "saved" data is lost if the program ends
- The "quit" mechanism is less confusing.
- The makefile has been corrected to work properly with Turbo
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.
- Some attribute names have been changed in the
- 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
- Improved descriptions were added for some tables and
A new version of laps works around a bug in some Level 2
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