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26 September 2024
- 18:3418:34, 26 September 2024 diff hist +895 N Run a Chemical Structure Search Created page with "# Go to Sample Libraries > Structure Search # Enter the ID of the compound you want to search against or draw the structure into the drawing canvas. You can alternately select a compound from a structure file by using the Open button from the drawing program. # Select the parameters to search on – #* Search Type (Similarity, Duplicate, Substructure) #* Library (Screenable Collection or Entire Collection) – Screenable Collection refers to the libraries that are still..." Tag: Visual edit
- 18:3318:33, 26 September 2024 diff hist +2,319 N Upload screening data Created page with "# Before uploading your screening data (primary or CRC), please ensure that you have entered your assay target (HTS Screens > Targets), method (HTS Screens > Methods), and controls (HTS Screens > Methods > Assay Details > Assay Controls) in MScreen. # Select HTS Screens > Primary Screens > Import data for uploading primary screening data and HTS Screens > CRC Screens > Import data for uploading CRC data. Enter an assay plate template for your assay by going to HTS Screen..." Tag: Visual edit
- 18:0918:09, 26 September 2024 diff hist +435 N Triage My Assay Data Created page with "# Go to '''HTS Screens > Search Activity''' # Select the Assay Parameter (e.g. Assay Target), Assay Criteria (e.g. 70% inhibition), and display option. Click ‘Submit’. Tip: When searching for activators in an inhibition assay, select a negative range (e.g. search in the -100 to -150% range). Define query as ‘between -150 and -100’. Ensure that the smaller value (-150) is the minima and the higher value (-100) is the maxima." Tag: Visual edit
- 18:0818:08, 26 September 2024 diff hist +6 Tutorials →User Tasks current Tag: Visual edit
- 18:0618:06, 26 September 2024 diff hist +171 Tutorials No edit summary Tag: Visual edit
- 18:0318:03, 26 September 2024 diff hist +12 Reformat 96-well stocks into 384 wells No edit summary current Tag: Visual edit
- 18:0218:02, 26 September 2024 diff hist +163 N Reformat 384-well stocks into 1536 wells Created page with "# Select '''Manage Plates > Reformat Plates''' and click on '''Option 2''' # Follow steps 2 to 5 from the 96-to-384 link" current Tag: Visual edit
- 18:0118:01, 26 September 2024 diff hist +1,656 N Reformat 96-well stocks into 384 wells Created page with "# Select Manage Plates > Reformat Plates and click on Option 1. # Select the parent plate library and set from the dropdown that contain the plates you would like to reformat. On selecting the sub set within the chosen library, MScreen populates the first and last plate ids for the chosen set. You can modify the plate id range by typing in your first and last parent plate ids. Click the ‘Select Plate’ button. # Enter the reformatting parameters: #* Freeze/Thaw – If..." Tag: Visual edit
- 18:0018:00, 26 September 2024 diff hist +1,984 N Cherrypick a hitlist for reconfirmation Created page with "# Select '''Manage Plates > Retest'''. #* Sample Source: There are three ways to provide a list of samples to be retested. Either upload a file, paste in a list, or select a small library (less than 500 samples) that contains the list of samples to be retested. You can combine two or even all three choices by checking on all the sources. #* Sample Screen: Selecting a screen for the uploaded retest samples helps to filter down the lots that had been tested in the selected..." current Tag: Visual edit
- 17:5817:58, 26 September 2024 diff hist +2,281 N Cherrypick a hitlist for CRC Created page with "# Select Manage Plates > Create CRC Plate. #* Sample Source: There are two ways to provide a list of samples to be cherrypicked for a CRC assay. Either upload a file or paste in a list that contains the list of samples to be cherrypicked. #* Sample Screen: Selecting a screen for the uploaded retest samples helps filter down the lots that have been tested in the selected screen. If no screen is selected, MScreen will list all the libraries and sets that contain the upload..." current Tag: Visual edit
- 17:5717:57, 26 September 2024 diff hist +16 Tutorials →Administrative Tasks Tag: Visual edit
- 17:5517:55, 26 September 2024 diff hist +699 N How does MScreen normalize the viability data on siRNA screens Created page with "MScreen gives users the option to identify Fluor (CTF) data and normalizes it against negative (100%) and lysed cells (0%) to compute viability by plate. $viability_percent = 100*($VDP – $lysed_plate_average)/($neg_control_plate_avg – $lysed_plate_average) $VDP = viability_data_part i.e. column that is identified to have the fluor data for viability computations $lysed_plate_average = average of lysed cell data per plate $neg_control_plate_avg=average of negativ..." current
- 17:5417:54, 26 September 2024 diff hist +1 How does MScreen apply value correction to assay data No edit summary current Tag: Visual edit: Switched
- 17:5317:53, 26 September 2024 diff hist +506 N How does MScreen apply value correction to assay data Created page with "The value correction in MScreen uses a quadratic linear regression-based correction, which may be applied to data that show uniform signal variation across rows or columns or the whole plate. MScreen uses row identifier (X) and column identifier (Y) and well identifier (W) for deriving the parameters (K, R, C, A, and B). CV = Z + M – (K + (X*R) + (Y*C) + ((W2)*A) + (W*B)) where CV is the corrected value, Z is the observed signal that needs to be corrected, and M is..." Tag: Visual edit
- 17:5017:50, 26 September 2024 diff hist +257 N What are the different types of chemoinformatics tools available Created page with "MScreen uses [https://openbabel.org/ Open Babel] for running chemical structure searches. Some other sources for structure searching are: # [https://pubchem.ncbi.nlm.nih.gov/ PubChem] # [https://zinc.docking.org/ ZINC] # [https://chem-space.com/ Chemspace]" current Tag: Visual edit
- 17:4417:44, 26 September 2024 diff hist +311 N What are the different types of reports available Created page with "The most common type of report is a triage report that is compiled after primary, confirmation, and CRC screens have been done. Please check this tutorial to upload and access the triage report for the screening target. The other types of reports are the target activity report and the library screening report." Tag: Visual edit
- 17:4317:43, 26 September 2024 diff hist −24 FAQ No edit summary current Tag: Visual edit
- 17:4117:41, 26 September 2024 diff hist +985 N What do the columns in an output file mean Created page with "# Compound Number – ID of the compound, substance or siRNA # Reactive_Filter_Flag – whether the sample hits a reactive filter (Red – R or Black – B) # Value # Percent_by_Assay # Percent_by_Plate # StDev_by_Assay # StDev_by_Plate # SD_Plate_by_Controls # SD_Assay_by_Controls # pAC50 # Active_Inactive_Indeterminate – whether sample was Active(A), Inactive (B) or Indeterminate (Q) # LOGP # CD_MOLWEIGHT # TPSA # BONDS # NAME_STRAIN_GENEID – Compound Name or Subst..." current
- 17:3917:39, 26 September 2024 diff hist +20 FAQ No edit summary
- 17:3817:38, 26 September 2024 diff hist +1,232 N What is Z' (read Z-factor) Created page with "The Z -factor calculation is useful during piloting for quality assessment of assay conditions (Zhang et. al. 1999). To quantitatively rank assay conditions, perform control experiments and calculate Z’ from the data collected: Z’ = 1 – 3*(SDpos+SDneg)/abs(Avpos-Avneg); SDpos = Standard Deviation of all positive control values SDneg = Standard Deviationof all negative control values Avpos = Average of all positive control values Avneg = Average of all..." current
- 17:2417:24, 26 September 2024 diff hist −5 What do the colors on the plate display mean No edit summary current
- 17:2417:24, 26 September 2024 diff hist +326 N What do the colors on the plate display mean Created page with "Primary Screen data are normalized to the average values of negative (0%) and positive (100%) controls and the percent values are color-coded by well (blue to red in increments of 20% activity – inhibition or stimulation). Progressively warmer colors represent higher levels of activity/inhibition based on the assay type."
- 17:2317:23, 26 September 2024 diff hist +32 FAQ No edit summary
- 17:1917:19, 26 September 2024 diff hist 0 What is pic50 or pac50 No edit summary current Tag: Visual edit
- 17:1817:18, 26 September 2024 diff hist +3 What is pic50 or pac50 No edit summary
- 17:1617:16, 26 September 2024 diff hist 0 FAQ No edit summary
- 17:1517:15, 26 September 2024 diff hist +909 N What is pic50 or pac50 Created page with "pIC50 and pAC50 are used to represent an Inhibition and Activation measure in log units for titration assays. RxPlora uses the term pIC50 even if it is an activation assay. pIC50 = -log(IC50). IC50 represents the compound/substance concentration required for 50% inhibition. Thus the larger the pIC50 the more potent the compound. A pIC50 of 4 indicates an IC50 of 10^4. A commonly used cut-off for defining potent compounds is a pIC50 >= 6 or a compound with submicromolar..." Tag: Visual edit: Switched
- 17:1417:14, 26 September 2024 diff hist +23 FAQ No edit summary Tag: Visual edit: Switched
- 17:0717:07, 26 September 2024 diff hist +4 FAQ No edit summary Tag: Visual edit: Switched
- 16:2216:22, 26 September 2024 diff hist +393 N FAQ Created page with "* What do the colors on the plate display mean? * What is Z' (read Z-factor)? * What is pIC50 or pAC50? * What do the columns in an output file mean? * What are the different types of reports available? * What are the different types of chemoinformatics tools available? * How does MScreen apply value correction to assay data? * How does MScreen normalize the viability data on siRNA screens?"
- 16:2016:20, 26 September 2024 diff hist −26 m Tutorials No edit summary Tag: Visual edit
- 16:2016:20, 26 September 2024 diff hist +583 N Tutorials Created page with "== User Tasks == How do I .. # Navigate the system - video # Find the hits on my target - video # Triage My Data # Upload screening data # Run a Chemical Structure Search # Get a summary report on my target # Curve-fit my CRC plate # Download activity on a list of compounds # Download compound structures # Enter my assay method into MScreen # Access the triage reports on my target == Administrative Tasks == How do I .. # Reformat 96-well stocks into 384 wells # Refor..."
- 16:1716:17, 26 September 2024 diff hist +13 MediaWiki:Sidebar No edit summary
- 15:0615:06, 26 September 2024 diff hist +10 MediaWiki:Sidebar No edit summary
- 15:0615:06, 26 September 2024 diff hist −23 MediaWiki:Sidebar No edit summary
- 15:0615:06, 26 September 2024 diff hist 0 MediaWiki:Sidebar No edit summary
- 15:0515:05, 26 September 2024 diff hist −69 MediaWiki:Sidebar No edit summary
- 15:0315:03, 26 September 2024 diff hist +178 N MediaWiki:Sidebar Created page with " * Resources ** mainpage|mainpage-description ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|help-mediawiki * Site Map * SEARCH * TOOLBOX * LANGUAGES"
- 14:5514:55, 26 September 2024 diff hist −12 Welcome No edit summary current
- 14:5414:54, 26 September 2024 diff hist +2,119 N Welcome Created page with "==MScreen== MScreen is an open source High Throughput Screening (HTS) data storage and analysis system that has been developed at the [https://www.lsi.umich.edu/science/centers-technologies/center-chemical-genomics Center for Chemical Genomics (CCG)], a core facility at the University of Michigan. MScreen processes HTS data through a web-based interface to help screeners visualize their data and simplify the hit-to-lead decision process. MScreen is available free of ch..."
- 14:5014:50, 26 September 2024 diff hist 0 m Docs:Welcome Docs admin moved page Welcome to Docs:Welcome
- 14:4614:46, 26 September 2024 diff hist 0 m Docs:Welcome Docs admin moved page Main Page to Welcome without leaving a redirect
- 14:4514:45, 26 September 2024 diff hist 0 m Docs:Welcome Docs admin moved page Docs:Welcome to Main Page over a redirect without leaving a redirect: revert
- 14:3914:39, 26 September 2024 diff hist +909 N Docs:What is pic50 or pac50 Created page with "pIC50 and pAC50 are used to represent an Inhibition and Activation measure in log units for titration assays. RxPlora uses the term pIC50 even if it is an activation assay. pIC50 = -log(IC50). IC50 represents the compound/substance concentration required for 50% inhibition. Thus the larger the pIC50 the more potent the compound. A pIC50 of 4 indicates an IC50 of 10^4. A commonly used cut-off for defining potent compounds is a pIC50 >= 6 or a compound with submicromolar..." current
- 14:1914:19, 26 September 2024 diff hist +1,149 m Docs:Welcome →MScreen
- 14:0814:08, 26 September 2024 diff hist −8 Docs:Welcome →Getting started
- 14:0814:08, 26 September 2024 diff hist +26 N Main Page Docs admin moved page Main Page to Docs:Welcome current Tag: New redirect
- 14:0814:08, 26 September 2024 diff hist 0 m Docs:Welcome Docs admin moved page Main Page to Docs:Welcome
- 14:0414:04, 26 September 2024 diff hist −137 Docs:Welcome No edit summary Tag: Visual edit
- 14:0414:04, 26 September 2024 diff hist +360 Docs:Welcome No edit summary Tag: Visual edit: Switched
