|
2017-02-09
February 9, 2017:
================
Important: major BAM update is released, version 2.1. If you wish to use new templates up to 2017 for your target sequences, you need to update BAM to 2.1. Older versions of BAM (lower than 2.1: 2.0.x.x) are NOT compatible with updated databases. The database format changed and requires application update. Older versions are still supported but with no database update.
2.1.0.0 version is released.
This update includes our significant efforts to keep BAM up to date and useful since we first published the paper in 2014. We updated all underlying databases up to the beginning of 2017. It allows to build your target models based on new templates. The database updates include Relational PDB database, PDBAA sequence database (default option if Uniref seq DB is not selected), sequence alignment profiles, etc.
Bug fixed: now BAM is capable to handle PDB chain templates having more than one character in a proper way; previously it only expected A, B, C, ... chains. Now it can properly process XX, XY, Xy, xy.
Improvements: more informative and condensed report messages are displayed if some sequence profiles are not available on our website for newer structures when BAM applicaton needs to download them on fly.
BAM Developers.
2016-05-04
May 4, 2016:
================
Pfam website moved and its previous one stopped serving Pfam domain search requests. With older versions of BAM users cannot search their sequences for Pfam domains. Please update BAM (BAM -> Tools -> Update).
2.0.15.0 version is released.
Improvement: Now E-value such as 0.001, 1e-5, 1e-7 for Pfam domain search can be specified instead of the previous default value of 10 (Tools -> Settings -> Online Servers -> Pfam E-value).
Bug fixed: The hardcoded value for Pfam website has been replaced with a dynamic setting. If the website moves again, it can be updated in Tools -> Settings -> Online Servers instead of releasing new hardcoded BAM update. The domain search and information requests work again.
BAM Developers.
2014-11-26
November 26, 2014:
================
New PDB relational database has been released. The previous version is more than one year old by now. IN ORDER TO COMPY WITH ITS NEW FORMAT, PLEASE 1) UPDATE BAM to the 2.0.14.0 version (BAM -> Tools -> Update) and then 2) update the PDB Relational Database itself (BAM -> Download/Update Databases -> Protein Relational Database).
2.0.14.0 version is released.
PLEASE UPDATE PRB RELATIONAL DATABASE AFTER UPDATING BAM TO 2.0.14.0 OTHERWISE NO ARCHITECTURES AND TEMPLATES WILL BE FOUND FOR ANY QUERY (BAM -> Download/Update Databases -> Protein Relational Database)
Update: PDBAA (PDB sequence database) has been updated to Nov-5-2014. It is a default option when no other large sequence database (like Uniref50 or Uniref90) is downloaded.
Update: PDB relational database has been updated. The previous one is more than one year old.
Bug fixed: In the 3D structure mode, the yellow spheres indicate locations of target sequence insertions into a template structure. Previously they were incorrectly shifted by one residue toward the C-terminus. The 3D graphical representation has been fixed. The alignment and its 2D representation were not effected in the previous versions. So it was only a 3D graphical problem. No computation results were effected.
Improvement: The total Pfam domain search timeout has been increased from 3 mins to 6.5 minutes with the same 10 attempts to accomodate the slowness of the Pfam webservice during its peak periods or slowness of Internet.
2014-06-18
June 18, 2014:
================
2.0.13.0 version is released.
Bug fixed: BAM relies on Pfam webservice from Trust Sanger Institute. This Pfam webservice became slower. It would not produce Pfam assignments to Target sequence(s) as fast as BAM would expect in past. As a result BAM would time out in some cases and would notify that no Pfam domains are found for Target. BAM's waiting logic for a Pfam response has been adjusted to accomodate for this 3rd provider change.
Bug fixed: PsiBlast execution would crash in some cases when it was run against larger, non-default sequence databases like Uniref50 or Uniref90. PDBAA is a default, small sequence database which did not cause these problems. The default PsiBlast parameters for log output have been changed to fix this problem.
Improvement: BAM is now capable to produce Target models based on Ca-only templates. An appropriate warning will pop up. If side-chain modeling is needed for such Ca-only models, their side chains can be modeled with our side-chain prediction software, SCWRL4 from a terminal after making Target backbone complete elsewhere.
Improvement: Tip message box is shown before running PsiBlast to notify the end users about fine-tuning PsiBlast.
2013-12-11
December 11, 2013:
================
2.0.12.2 version is released.
Now 4 out of 5 sample projects have a complete set of files of a full round of homology modeling. Users can refer to these files for learning and understanding what to expect. The 5th sample project is left with an input sequence file only. It is done on purpose so that the users can try to work with it from scratch.
PDBAA (PDB sequence database) has been updated. It is a default option when no other large database is downloaded.
Bug fixed: new templates cannot be calculated when Compute button is clicked. It happens when the user is complete with the first project and switches to the second one during the same BAM session.
Bug fixed: editing a sample sequence file would force to save it under a new filename and under a new project folder.
2013-11-21
November 21, 2013:
================
2.0.12.1 version is released.
BAM, Release Candidate is available to general public.
2013-10-08
October 8, 2013:
================
BAM, Beta version is available to general public. It supports auto-updating and urgent messages.
2013-09-24
September 24, 2013:
================
BAM should run successfully on any Windows platform, including XP 32/64, Vista 32/64, Windows 7 64, Windows 8 64.
Few improvements in GUI of BAM itself and BAM Updater.
2013-08-27
August 27, 2013:
================
BAM updater development is complete. It is ready for internal testing.
2013-08-22
August 22, 2013:
================
A feature to flag developers' urgent messages as Read is added.
2013-08-21
August 21, 2013:
================
A system for urgent messages from the BAM developers is complete.
2013-08-16
August 16, 2013:
================
BAM is in a pre-release state.
Please check for updates from within BAM application itself by going to BAM -> Main Menu -> Reinstall/Update BAM.
back to top
|
