Timeline



02/26/2015:

20:55 GritsChangeLog created by Rene Ranzinger
20:31 Ticket #264 (MS converter: Error when canceling) closed by Rene Ranzinger

02/25/2015:

20:15 Ticket #264 (MS converter: Error when canceling) created by Rene Ranzinger
If the cancel button is pressed in the converter dialog: * Exceptions …
20:11 Ticket #252 (MS converter: Overwriting files) closed by Rene Ranzinger
20:00 Ticket #263 (Processmanager) created by Rene Ranzinger
Create a generic process manager that can be used to run time …
19:57 Ticket #262 (MS Editor: Redesign of file handling) created by Rene Ranzinger
Creation Wizard * Move the MS type on the first page * Remove second …
19:51 Ticket #261 (Prevent multiuse of workspace) created by Rene Ranzinger
A workspace should be opened only by one GRITS instance at a time.
19:50 Ticket #248 (Scale bar for Cartoon preference does not have enough options) closed by Rene Ranzinger
18:53 Ticket #260 (Unable to handle Direct Infusion if no MS1 scan present) closed by Rene Ranzinger
18:53 Ticket #192 (MS Editor: Inconsistency when presenting different MS types) closed by Rene Ranzinger
18:26 Ticket #260 (Unable to handle Direct Infusion if no MS1 scan present) created by dbrentw
If the user creates a direct infusion MS file but does not generate a …
17:54 Ticket #259 (Configuraiton location) closed by Rene Ranzinger
17:53 Ticket #259 (Configuraiton location) created by Rene Ranzinger
Change config file location to prevent the loose of files when …
16:36 Ticket #258 (Experiment designer: Configuration in jar) created by Rene Ranzinger
* Keep the global ontology in the jar rather than copying it to the …
00:29 Milestone Plugin - Sample Manager 1.0 completed
First version of the sample manager plugin which replaces the old …
00:29 Ticket #256 (Sample Editor: Editing String descriptors) closed by Rene Ranzinger
00:25 Ticket #257 (Migrate to Eclipse Luna (4.4)) created by Rene Ranzinger
Migrate to the newest Eclipse version.
00:17 Ticket #157 (Sample management: Icon problems) closed by Rene Ranzinger

02/24/2015:

23:56 Ticket #221 (Sample Editor: Store namespace and IDs for descriptors) closed by Rene Ranzinger
23:47 Ticket #256 (Sample Editor: Editing String descriptors) created by Rene Ranzinger
When editing string descriptors (double click) a dialog opens with the …
23:35 Ticket #235 (MS Editor: Web service invocation problem) closed by Rene Ranzinger
23:31 Ticket #240 (Create New Sample: Wizard) closed by Rene Ranzinger
23:16 Ticket #233 (GELATO: Cancel) closed by Rene Ranzinger
23:11 Ticket #255 (Support mzML) created by Rene Ranzinger
In addition to mzXML we should also mzML files. Probably best to …
23:06 Ticket #251 (Displaying data in Spectra tab correctly) closed by Rene Ranzinger
23:01 Ticket #254 (Optimizing opening MS annotation) created by Rene Ranzinger
When opening (double click) a annotated MS1 scan the first operation …
22:53 Ticket #244 (Better icons for experiment designer) closed by Rene Ranzinger
18:42 Ticket #253 (MS Editor: Missing MS1 scans for direct infusion) closed by Rene Ranzinger
18:31 Ticket #253 (MS Editor: Missing MS1 scans for direct infusion) created by Rene Ranzinger
If a direct infusion experiment is recorded without MS1 the upload …
18:07 Ticket #252 (MS converter: Overwriting files) created by Rene Ranzinger
If file name for Full MS and MS data is the same e.g.: * Data folder …
17:56 Ticket #251 (Displaying data in Spectra tab correctly) created by dbrentw
The Spectra chart has the ability to display data in either profile or …
16:23 Ticket #65 (Sample manager - Unit of Measurement) closed by Rene Ranzinger

02/23/2015:

23:37 Ticket #246 (Error saving annotations for LC-MS) closed by Rene Ranzinger
23:34 Ticket #247 (Checkboxes not working for Summary View for MS Profile data) closed by Rene Ranzinger
23:32 Ticket #250 (Error trying to use Filter open for MS Annotation of LC-MS data) closed by Rene Ranzinger
23:24 Ticket #15 (New icon and splash screen) closed by Rene Ranzinger
21:44 Ticket #250 (Error trying to use Filter open for MS Annotation of LC-MS data) created by dbrentw
If you open an LC-MS annotation and attempt to use the "Filter" tool …
17:08 Ticket #162 (Experiment desiger: User guide) closed by Rene Ranzinger

02/21/2015:

00:00 Ticket #245 (Annotation Editor: Hide/show peaks in Summary) closed by Rene Ranzinger

02/20/2015:

23:59 Ticket #249 (Sample Editor - manager: Display issues on Mac) created by Rene Ranzinger
When opening the manager (admin/user) on Mac: * there is a big space …
21:31 Ticket #248 (Scale bar for Cartoon preference does not have enough options) created by dbrentw
The scale of the cartoon preference only allows for a few size …
21:26 Ticket #247 (Checkboxes not working for Summary View for MS Profile data) created by dbrentw
If you open the Summary view for MS Profile annotation, you can click …
21:23 Ticket #246 (Error saving annotations for LC-MS) created by dbrentw
If you edit the selected annotations for LC-MS and try to save, an …
01:06 Ticket #234 (Annotation Editor: Direct infusion Num Annotation peaks) closed by Rene Ranzinger
01:03 Ticket #231 (LC/MS annotation entry) closed by Rene Ranzinger
01:01 Ticket #245 (Annotation Editor: Hide/show peaks in Summary) created by Rene Ranzinger
Tested with Khoo data 5% cutoff and BY ions. * Open Scan 5 or 8 in …
00:45 Ticket #204 (LC-MS data: Unable to open MS2) closed by Rene Ranzinger

02/19/2015:

16:31 Ticket #244 (Better icons for experiment designer) created by sena
Need better icons for experiment template "save as" and protocol …
00:03 Ticket #222 (Sample Editor: Disallow invalid values for Type-ahead) closed by Rene Ranzinger

02/18/2015:

23:44 Ticket #36 (Better edit icon in sample editor) closed by Rene Ranzinger
22:58 Ticket #203 (LC-MS data: unannotated spectra) closed by Rene Ranzinger
22:53 Ticket #202 (LC-MS data: Num of Annotated peaks incorrect) closed by Rene Ranzinger
22:46 Ticket #243 (Batch annotation of several MS runs) created by Rene Ranzinger
Allow to select several MS entries and to annotate them with the same …
22:43 Ticket #242 (Batch creation of sample, experiment design and MS entries) created by Rene Ranzinger
Allow to create a batch of samples, experiment designs and MS entries …
22:36 Ticket #241 (Rename of entries) created by Rene Ranzinger
Create a right click (project explorer) and edit menu based option to …
22:29 Ticket #240 (Create New Sample: Wizard) created by Rene Ranzinger
Change the sample/analyte creation dialog to a wizard. * first page: …
17:22 GritsTutorial_ExperimentDesignerInterface edited by sena
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17:14 GritsTutorial_ExperimentDesignerInterface edited by sena
(diff)
17:12 GritsTutorial_ExperimentDesignerInterface created by sena
16:58 TutorialGrits edited by sena
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02/17/2015:

20:25 Ticket #239 (Worspace Chooser - no Shortcuts) created by Rene Ranzinger
Discovered one "issue?" with the GRITS Toolbox "Select Workspace" > …
03:36 Ticket #220 (Exception while opening sample editor) closed by Rene Ranzinger

02/16/2015:

23:01 Ticket #238 (Determine how to model glycan structures in the graph) created by sena
Need to determine whether gylcans can be rendered in the graph …
22:58 Ticket #237 (Determine the technology to be used to implement the Glycan pathway module) created by sena
Investigate the capabilities provided by ZEST to see if it is more …
22:13 Ticket #227 (Sample Editor: NamespaceHandler for NCBI) closed by Rene Ranzinger
22:00 Ticket #229 (Creating new Analyte: First component name) closed by Rene Ranzinger
22:00 Ticket #59 (Icons in sample manager) closed by Rene Ranzinger

02/13/2015:

23:54 Grits_IconsDocumentation edited by shan
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23:54 pencil-icon.png attached to Grits_IconsDocumentation by shan
23:51 pencil-red-icon.png attached to Grits_IconsDocumentation by shan
23:21 Grits_IconsDocumentation edited by shan
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23:16 Edit-icon.png attached to Grits_IconsDocumentation by shan
23:15 Grits_IconsDocumentation created by shan
18:52 GritsDocumentation edited by shan
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18:52 TutorialGrits edited by shan
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02/12/2015:

23:24 Ticket #214 (MS Editor: Fusion data) closed by Rene Ranzinger
23:23 Ticket #236 (GRITS not reacting when viewing MS and annotation data) created by Rene Ranzinger
When opening large data sets (e.g. Lindas Fusion data or Khoo data) …
23:10 Ticket #235 (MS Editor: Web service invocation problem) created by Rene Ranzinger
There errors may have been introduced by changes with ticket #152. * …
20:43 Ticket #152 (Max upload size for mzXML web service) closed by Rene Ranzinger
20:40 Ticket #215 (MS Editor: MSProfile data) closed by Rene Ranzinger
20:38 Ticket #234 (Annotation Editor: Direct infusion Num Annotation peaks) created by Rene Ranzinger
For direct infusion annotation runs the Num Annotation Peaks column is …
20:28 Ticket #232 (GELATO: Temp folder managment) closed by Rene Ranzinger
20:19 Ticket #233 (GELATO: Cancel) created by Rene Ranzinger
When canceling an annotation run (after glycan DB initialization): - …
18:08 Ticket #232 (GELATO: Temp folder managment) created by Rene Ranzinger
Problem 1: GELATO creates a new folder for each annotation run but it …
17:54 Ticket #231 (LC/MS annotation entry) created by Rene Ranzinger
When deleting an LC/MS annotation the zip archive in the ms folder is …
17:37 Ticket #230 (support iCRM) created by dbrentw
00:30 Ticket #226 (Annotation Editor: Open MS profile data) closed by Rene Ranzinger
00:05 Ticket #201 (LC-MS data: Missing MS1 scans) closed by Rene Ranzinger

02/11/2015:

23:55 Milestone Plugin - Experiment Designer 1.0 completed
First version of the experiment designer plugin. This plugin will …
23:54 Ticket #211 (Experiment designer: Predeployment of variants) closed by Rene Ranzinger
23:47 Ticket #223 (Experiment designer: Deployment) closed by Rene Ranzinger
00:59 Ticket #229 (Creating new Analyte: First component name) created by Rene Ranzinger
The name of the first component, which is auto created with the …
00:55 Ticket #196 (Sample editor : Add Descriptor) closed by Rene Ranzinger
00:44 Ticket #95 (Sample Manager : All sections same size in right side) closed by Rene Ranzinger
00:43 Ticket #198 (Sample manager - Procedure for new Namespace) closed by Rene Ranzinger
00:37 Ticket #183 (Sample PDF Report) closed by Rene Ranzinger
00:11 Ticket #224 (Intensity filter not working for MS1 scans) closed by Rene Ranzinger
00:10 Ticket #225 (GELATO: Right click for Annotation entry) closed by Rene Ranzinger

02/09/2015:

22:07 Ticket #228 (Need 2 intensity cutoffs for MS Annotation (MS1 and MSn)) created by dbrentw
It turns out that the intensity percentage filter was only applied to …
18:39 Ticket #227 (Sample Editor: NamespaceHandler for NCBI) created by shan
The generic NamespaceHandler crashes for for the species namespace …
00:33 Ticket #179 (MS annotation does not open) closed by Rene Ranzinger
00:30 Ticket #226 (Annotation Editor: Open MS profile data) created by Rene Ranzinger
After opening MS profile annotation data the "Structure Annotation" …
00:25 Ticket #225 (GELATO: Right click for Annotation entry) created by Rene Ranzinger
* In the Project explorer right click on an annotation entry * Select …
00:20 Ticket #216 (MS Editor: MSProfile data 2) closed by Rene Ranzinger
00:18 Ticket #200 (GELATO: Intensity Cut-off should be a double) closed by Rene Ranzinger
00:17 Ticket #155 (Double values for Intensity cutoff in GELATO) closed by Rene Ranzinger
00:16 Ticket #148 (MS profile support in GELATO) closed by Rene Ranzinger

02/07/2015:

16:45 Ticket #224 (Intensity filter not working for MS1 scans) created by dbrentw
When applying the intensity cutoff filter for MS annotation, it …
00:25 Ticket #223 (Experiment designer: Deployment) created by Rene Ranzinger
After making a new deployment and trying to create a new design a …
00:06 Ticket #219 (Experiment designer: Set template when creating new template) closed by Rene Ranzinger

02/06/2015:

23:09 Ticket #222 (Sample Editor: Disallow invalid values for Type-ahead) created by Rene Ranzinger
In the new/edit descriptor dialog is it possible to type a incorrect …
23:01 Ticket #221 (Sample Editor: Store namespace and IDs for descriptors) created by Rene Ranzinger
In the sample XML file for each descriptor the ID, selected namespace …
22:51 Ticket #220 (Exception while opening sample editor) created by sena
I see NullPointerException in the log file whenever I open the sample …
22:43 Ticket #218 (Experiment designer: Delete file error) closed by Rene Ranzinger
22:41 Ticket #41 (Change namespace of dosage) closed by Rene Ranzinger
22:38 Ticket #195 (Sample Editor: Tooltip on rows) closed by Rene Ranzinger
22:09 DevelopmentNotes_ExperimentDesigner edited by sena
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19:41 Ticket #210 (Experiment designer: Delete selected items) closed by Rene Ranzinger
19:40 Ticket #219 (Experiment designer: Set template when creating new template) created by Rene Ranzinger
Problem: * Create new protocol in editor from template x * Remove/add …
19:33 Ticket #207 (Experiment designer: Protocol URI) closed by Rene Ranzinger
19:29 GritsTutorial_PDFGeneration edited by sena
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02/05/2015:

18:43 GritsTutorial_AddingNewNamespaceForDescriptorValue edited by shan
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17:40 ExperimentDesignerProtocolVariants created by sena
17:26 GritsDocumentation edited by sena
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01:02 Ticket #218 (Experiment designer: Delete file error) created by Rene Ranzinger
* Create new sample * Create new design with several protocols => …
00:21 TutorialGrits edited by shan
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00:21 GritsTutorial_AddingNewNamespaceForDescriptorValue created by shan

02/04/2015:

23:44 Ticket #205 (Experiment desiger: Adding data containing steps) closed by Rene Ranzinger
23:39 Ticket #217 (Experiment designer: Box size) closed by Rene Ranzinger
23:38 Ticket #212 (Experiment designer: Description when creating templates) closed by Rene Ranzinger
19:13 TutorialGrits edited by shan
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19:12 GritsTutorial_UpdateNamespaces edited by shan
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19:08 CellTypeDownload.png attached to GritsTutorial_UpdateNamespaces by shan
19:08 GritsTutorial_UpdateNamespaces created by shan
18:46 GritsTutorial_NamespaceHandlingForTypeahead created by shan
16:51 TutorialGrits edited by shan
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13:09 GritsTutorial_MSMethodCreatoin edited by dbrentw
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13:05 GritsTutorial_MSMethodCreatoin edited by dbrentw
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00:22 GritsTutorial_MSMethodCreatoin edited by dbrentw
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00:15 GritsTutorial_MSMethodCreatoin edited by dbrentw
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02/03/2015:

23:24 Ticket #145 (Sample editor : Find matching Template for a Component) closed by Rene Ranzinger
22:53 Ticket #213 (Sample Editor: Remove download feature) closed by Rene Ranzinger
22:52 Ticket #197 (Sample manager - Namespace) closed by Rene Ranzinger
22:41 Ticket #209 (Experiment designer: Dublicated protocol templates) closed by Rene Ranzinger
22:22 Ticket #217 (Experiment designer: Box size) created by Rene Ranzinger
* Select a protocol from the Palette * Click in the drawing area and …
22:16 Ticket #208 (Experiment designer: Editable units) closed by Rene Ranzinger
22:14 Ticket #206 (Experiment designer: Web URL) closed by Rene Ranzinger
19:19 Ticket #216 (MS Editor: MSProfile data 2) created by Rene Ranzinger
After converting the mzXML file from ticket #215 to mzML and back to …
02:14 Ticket #215 (MS Editor: MSProfile data) created by Rene Ranzinger
Trying to open the Maldi data from Roberto …
01:53 Ticket #214 (MS Editor: Fusion data) created by Rene Ranzinger
Trying to run Lindas data on GRITS I got two problems besides the …

02/01/2015:

23:12 Ticket #213 (Sample Editor: Remove download feature) created by Rene Ranzinger
Remove the download button and code from the plugin.
23:07 Ticket #212 (Experiment designer: Description when creating templates) created by Rene Ranzinger
When creating a new template of a protocol with Description field …
23:03 Ticket #211 (Experiment designer: Predeployment of variants) created by Rene Ranzinger
It should be possible to store a list of variants as part of the …
22:57 Ticket #210 (Experiment designer: Delete selected items) created by Rene Ranzinger
If the "delete" button on the keyboard is pressed and the editor is …
22:51 Ticket #209 (Experiment designer: Dublicated protocol templates) created by Rene Ranzinger
Create a new protocol and give it the name "Tyrpsin digestion". This …
22:46 Ticket #208 (Experiment designer: Editable units) created by Rene Ranzinger
* Choose a parameter with unit of measurement * Click in the cell …
21:35 Ticket #207 (Experiment designer: Protocol URI) created by Rene Ranzinger
Each protocol has two URIs 1. URI of the template used to instantiate …
21:31 Ticket #206 (Experiment designer: Web URL) created by Rene Ranzinger
Add a member variable for a URL in the data-model of protocal and in …

01/31/2015:

03:25 Ticket #205 (Experiment desiger: Adding data containing steps) created by Rene Ranzinger
If an step with data (MS) is added after the experimental design is …
03:21 Ticket #191 (Report generation: Overwrite) closed by Rene Ranzinger
03:20 Ticket #116 (Experiment designer: Report generation) closed by Rene Ranzinger
03:10 Ticket #136 (Out of Memory when dealing with LC/MS runs) closed by Rene Ranzinger
03:10 Ticket #154 (Khoo data set) closed by Rene Ranzinger
03:09 Ticket #147 (LC-MS/MS support in GELATO) closed by Rene Ranzinger
03:08 Ticket #204 (LC-MS data: Unable to open MS2) created by Rene Ranzinger
Double clicking on MS2 precursor in MS shows error message about not …
02:59 Ticket #203 (LC-MS data: unannotated spectra) created by Rene Ranzinger
* Open an MS1 that has unannotated precursors * Change to MS Scans tab …
02:54 Ticket #202 (LC-MS data: Num of Annotated peaks incorrect) created by Rene Ranzinger
In annotation editor (MS Scans tab) the column "Num Annotated Peaks" …
02:46 Ticket #201 (LC-MS data: Missing MS1 scans) created by Rene Ranzinger
In annotation editor (MS Scans) several MS1 that do not have subscans …
00:37 Ticket #200 (GELATO: Intensity Cut-off should be a double) created by Rene Ranzinger
Change intensity cut off in the dialog and the data model from integer …
00:28 Ticket #199 (MS Editor: Progress bar for creating new MS entries) created by Rene Ranzinger
Add a progress bar when creating new MS entries, since copying large …

01/30/2015:

21:53 Milestone Plugin - GlycoVault 1.0 completed
A plugin for the interaction with the GlycoVault database: * Creation …
21:52 Ticket #176 (GlycovaultManager : Download SourceSample) closed by Rene Ranzinger
21:48 Tickets #170,​174,​105,​106,​112,​113,​120,​171,​172,​175,​177,​178,​107,​108,​114 batch updated by Rene Ranzinger
18:31 Ticket #198 (Sample manager - Procedure for new Namespace) created by shan
* Document the procedure in wiki * Add files names to ontology by …
18:16 Ticket #197 (Sample manager - Namespace) created by shan
Namespace for Genes and Treatment should be changed to string
18:13 Ticket #196 (Sample editor : Add Descriptor) created by shan
When adding a descriptor implement : * Implement Dialog as a …
00:46 Ticket #103 (Dictionary control for descriptor values) closed by Rene Ranzinger
00:44 Ticket #195 (Sample Editor: Tooltip on rows) created by Rene Ranzinger
- Remove the "-" after the descriptor name - Add a paragraph with the …
00:39 Ticket #104 (Type ahead for descriptor values) closed by Rene Ranzinger
00:29 Ticket #194 (MS data: Scan hierarchy view) created by Rene Ranzinger
Add a view in the left side area (Project Explorer View) when opening …
00:26 Ticket #193 (MS Editor: Precursor column) created by Rene Ranzinger
In the "MS Scans" tab of the MS editor add a column precursor m/z. …
00:23 Ticket #192 (MS Editor: Inconsistency when presenting different MS types) created by Rene Ranzinger
Open direct infusion in MS Editor shows the following tabs: - List of …
00:11 Ticket #180 (Opening TIM experiments) closed by Rene Ranzinger

01/29/2015:

23:51 Ticket #173 (Incorrect object returned from glycovault client's getProtocolList() method) closed by Rene Ranzinger
21:26 Ticket #191 (Report generation: Overwrite) created by Rene Ranzinger
If a PDF report is generated and an existing file name is chosen a …
20:41 Ticket #80 (Icons for views and editor) closed by Rene Ranzinger
20:40 Ticket #167 (Paper view - invalid PMID) closed by Rene Ranzinger
20:28 GritsTutorial_MSMethodCreatoin edited by dbrentw
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20:27 GritsTutorial_MSMethodCreatoin edited by dbrentw
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17:03 GritsTutorial_MSMethodCreatoin created by dbrentw
17:02 TutorialGrits edited by dbrentw
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01:34 Ticket #190 (Distinguish isomeric structures) created by Rene Ranzinger
Implement strategies to distinguish isomeric structures or find …
01:30 Ticket #189 (JMass: Deconvolution and deisotopic) created by Rene Ranzinger
Use the JMass code and the matched simulated data to deconvolute and …
01:04 Ticket #188 (JMass: Simulation of MS1 data) created by Rene Ranzinger
Integrate JMass to simulate MS1 data: - Calculate an alignment score …
00:55 Ticket #187 (SAGE integration) created by Rene Ranzinger
Integrate of SAGE (https://code.google.com/p/sage-and-gelato/) into …
00:51 Ticket #186 (MS data: user guidelines) created by Rene Ranzinger
Creation of user guidelines similar to the experiment designer …
00:48 Ticket #185 (Glycan centric representation of data) created by Rene Ranzinger
MS annotation table and merge table are both peak centric. An …
00:45 Ticket #184 (Scrolling problem) created by Rene Ranzinger
In MS tables the vertical scroll bar does not really show the length …

01/28/2015:

23:09 Ticket #183 (Sample PDF Report) created by Rene Ranzinger
Add a module to the Experiment designer PDF report generation to add …
21:34 Ticket #182 (MS Quantification) created by Rene Ranzinger
- Quantification against internal standard - Intensity as ration (%) …
21:31 Ticket #181 (Add key numbers columns to merge) created by Rene Ranzinger
Key number columns (glycan type, number of branches, number of gal-gal …
20:44 GritsTutorial_PDFGeneration edited by sena
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20:30 GritsTutorial_PDFGeneration created by sena
19:43 TutorialGrits edited by sena
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