ChemBank Release Notes
2.1.8
New Features and Bugs Fixed
- CBNK-23 - User filtering by last name now available.
- CBNK-32 - 12 Compounds without sources associated to correct source. Source is now required for compounds.
- CBNK-33 - Search by user list will now warn the user if they go over the maximum of 1000 items per category.
- CBNK-34 - Fixed a problem with listing some incorrect PubMed links on Biochemical Interactions for some molecules.
2.1.7
New Features and Bugs Fixed
- Biological, biochemical, and therapeutic annotations on molecules now have corresponding PubMed document links.
- A more permanent assay URL is now available using the experiment number (xn) parameter.
2.1.6
New Features and Bugs Fixed
- A new ChemBank User Guide has been published to the website.
- The ChemBank help has been updated.
- Errors when trying to view proteins have been fixed.
2.1.5
Bugs Fixed
- The multi-assay heatmap visualization download filters out columns of all NAN data now.
- The multi-assay heatmap visualization assay link double-click in IE has been fixed.
- The assay type filter has been fixed.
- The plate heatmap and histogram pages drop-down selects now use consistent names with the scatterplot.
2.1.4
New Features
Molecule Search
- Users can now search by virtual id in the user list search.
Miscellaneous Changes
- Enhancements to name curation were made.
- Database merge completed.
2.1.3
New Features
Molecule Search
- Users can now filter out molecules which are known to be
autofluorescent. This feature is available on the search by assay
page.
- Search results now display the primary name and autofluorescence characteristics (if known) for each search result.
- A new search by user list page is now available. This page
supports searches by lists of molecule names, SMILES, plate/well
specifications, or ChemBankIds.
Visualization
- The data shown in the multi-assay molecule feature heatmap can now be downloaded by selecting the [download data] link.
Web Services
- There are now web services which support downloading of all
project, assay, and well performance data. Additionally,
substructure and similarity search are supported. Pointers to the
web services wsdl files can be found on the web services page. There is also a link to this page in the footer.
View Molecule
Page
- The google search functionality has been expanded to include all
molecule names, SMILES, InChI, and any functional annotations to the
molecule.
- Visualizations detailing the autofluorescence of molecules are
shown when available. Details on the autofluorescence method can
be found in the help.
Molecular Descriptors
- Two new structure-based descriptors have been added.
These are # of Lipisnki Violations (defined as number of
Rule-of-5 Violations for the descriptors Molecular Weight, LogP by
GhoseCrippen, HBond Donors and HBond Acceptors) and Veber
Compliance (of descriptors Rotatable Bonds, Polar Surface Area, HBond
Donors and HBond Acceptors). As with any other descriptor,
molecule searches can be conducted restricting resultant molecules to
user defined ranges of these descriptors.
Bugs Fixed
- Heatmap jar size has been dramatically reduced.
- When using the back button to choose different assay features for
the heatmap, sometimes the assay selection would not take or would be
incorrect.
- Clicking the verify registration link more than once would result in an error.
- Back slashes lost on SMILES popup on view molecule page.
- Molecule depictions occasionally incorrect on search results page.
- Heatmap sorting always put non-tested compounds at before the
high value when sorting by assay performance. This made it
difficult to make use of the sorting. Non-tested compounds now
will sort to the end of the list.
2.1.2
New Features
Visualization
- Scatter plots are now interactive. To select a
sub-region of interest, click on the scatter plot image and drag the
mouse until the dashed box outlines the region. After
selecting a region, it will be surrounded with a gray square and the
coordinates will be displayed in a text box to the left of the image.
Users may then view the list of molecules selected ([view molecules in range as list])
or zoom into the selected region ([resample scatterplot using this
range]).
- A new multi-assay molecule feature heatmap visualization
has been added.
This visualization is the first of new features
targeted at
cross-sectional analysis of ChemBank
data. Using this Java applet, users can
view the list of molecules from a search across all screens within ChemBank.
Click here
for an example. See the help
for a more detailed description of how this visualization works.
Protein
- Proteins can now be used as an entry point for exploring
data in ChemBank.
- Users may search for proteins by name, synonyms,
description, Entrez Gene Id, GenBank Accession Number, Species, NCBI
reference
sequence, and PDB Id.
- The view protein page contains a list of binding events
identified by small-molecule microarray (SMM) experiments.
- The view protein page contains links to all assays which
used the protein in some capacity.
- On the view assay page, proteins used by that assay in some
capacity will have a
link to the protein's page.
- On
the view molecule page, biochemical
interactions involving a known protein will contain a link to the
protein's page.
- For more information on
protein related
functionality in ChemBank,
see the help
page.
Molecule Search
- Molecule search results no longer contain virtual
stereochemical "parent" (i.e.,
stereofree) versions of molecules.
- The project and assay pages now have an easy way to find
all molecules that were Standard Hits by clicking on the ([find
hits]) link.
- Search for molecules by assay results has been enhanced. On
the molecule search by assay page, a new radio button for finding all
molecules tested in an assay
or project (regardless of its performance in the assay or project) is
now present.
Assay Search
- The assay search results page now shows more detail about
the assay and its parent project. Results are sorted first by project
name and then by assay name.
View Molecule
Page
- Next to each InChI molecule
name is a link
titled [Google
InChI Search]. Clicking on this
link will open
a Google search page for the InChI string.
Bugs Fixed
- The between operator for
the search molecule by
assay page has been fixed.
- The english description for
"molecule search by
assay" searches
has been improved.
- The minimum value for the
Histogram x-axis
display after subregions are selected is now properly set.
- The Histogram uses the same
bin widths when
displaying mock and compound-treatment data distributions.
- The intermittent error seen
on Internet
Explorer when
trying to conduct search molecule by assay has been fixed.
This error would manifest with the IE error message "cannot
open the requested site -- Operation aborted".
- The
screening
data download now gives feedback to the user more quickly.
2.1.1.5
New
Features
Assay Type
-
Assays are now categorized into the
following types: HTS (homogeneous), HTS (cell-based), HTS
(microorganism), HTS (whole organism), gene-expression HTS,
small-molecule microarray, and high-content screen.
-
Assay type is displayed for each
item in the "Screening Test Instances" table of the "View Molecule"
page.
-
The assay search page and results
screen now allow for assay type.
Bugs
Fixed
-
Bug in molecule depiction could
sometimes cause general website performance problems.
- If
the list of projects is filtered, and the user selects all filtered
projects, then the search was incorrectly done across all assays in all
projects.
- Tversky
similarity search now working.
- Assay
results search descriptions are now more precise.
2.1.1
New
Features
Visualization
-
Context aware histogram
visualization. When navigating to a histogram visualization
via a view molecule page (by clicking on the assay, then histogram
links), the position of the molecule's scores will be displayed.
-
Context aware scatter plot
visualization. When navigating to a scatter plot
visualization via a view molecule page (by clicking on the assay, then
scatter plot links), the position of the molecule's scores will be
displayed.
-
Context aware plate heatmap
visualization. When navigating to a plate view from the view
molecule page, the position of the molecule in the plate is hilighted.
-
Histogram and scatter plot
visualizations can be bookmarked. All data required to
generate the histogram and scatter plot visualizations is now included
in the http address for the page. This allows the
visualizations to be bookmarked and fixes some bugs related to use of
the back button and visualizations.
Search
-
Search across all projects and
assays now supported. Molecule searches can now contain
criteria which find all molecules which hit in any screen or in a
user-specified subset of screens. The search by assay page of
molecule search now allows interactive selection of multiple projects
and assays as well as filtering of the selectable list, all on one
page. By combining this feature with other criterion, it is
now possible to create searches like "Find all hits by chemist x." or
"Find all hits with project x."
Data Download
-
Screening data can now be
downloaded. All screening data for a project or assay may now
be downloaded. This data is available via a link on the
individual view-project or view-assays pages. Detail
regarding the format and content is available on the Help
page. This function has replaced the display of actual screening
results on molecule search results pages.
Bugs
Fixed
-
/screens forwards to
view-projects.htm. Prior to ChemBank 2.0, the /screens page
provided the list of screens within ChemBank. The equivalent
of this list is now available under
/assays/view-projects.htm. The /screens link will forward to
this new page for compatibility reasons.
-
Forced logins now redirect to the
original page after the user logs in.
-
Composite Z scores were missing for
plate replicates other than A and B.
-
Speed improvements on view molecule
page.
-
Acknowledgements for ChemBank 1.2
team members added.
2.1.0
New Features
General
- All
tables can now be sorted by any column in the table. Simply
click on the header for a column to sort in ascending order.
Click again to sort in descending order. This feature does
not apply to compound or assay search results.
View
Molecule page
- Well
location, ZScore, CompositeZ, and Standard Hit values were added to the
Screening Test Instances table.
- Virtual
IDs (an identifier for each "instance" of a molecule) and Pubchem
substance links were added to the Stock Plate/Well locations table.
- The
name type for each displayed name is now shown in italics in
parentheses after each name.
View
Projects page
- The
number of standard hits and and the number of compounds screened are
shown for each project.
View
Project page
- The
number of standard hits and the number of compounds screened are shown.
Molecule
name curation
- New
interfaces to support curation of molecule names have been
added. These interfaces will allow the ChemBank curation team
to improve the state and coverage of molecule names over the coming
weeks.
Bugs Fixed
- Disabled
email account cannot be changed.
- Browser
form auto-fill causes problems.
- Double
verification of registration looks like an error.
- Logout
and My Account links disappear on wide browsers.
- Names,
SMILES, and InChI line wrapping broken on Firefox.
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