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- 19:46, 26 September 2024 Access the triage reports on my target (hist | edit) [416 bytes] Docs admin (talk | contribs) (Created page with "# Select '''HTS Screens > Targets > All Targets''' # Enter the full or partial name of the target in the search box and click ‘Search’ to get the triage report. # MScreen displays the list of targets that meet your search criteria; click on a row to view the target’s details. # Click the ‘Triage Reports’ tab to view the list of triage reports that have been uploaded into MScreen.") Tag: Visual edit
- 19:27, 26 September 2024 Enter my assay method into MScreen (hist | edit) [894 bytes] Docs admin (talk | contribs) (Created page with "# Go to '''HTS Screens > Methods > Assay Methods (SOPs)''' and search for your method’s name by typing the first few characters in the search box and clicking the ‘Search’ button. # If your assay method is listed in the search results, click on it. If not, click the ‘Add Assay Method’ link in the top left-hand corner to add your assay method to MScreen. Use an intuitive name in the ‘METHOD’ field. Leave the ‘FILEVERSION’ field blank and select the corre...") Tag: Visual edit
- 19:22, 26 September 2024 Download compound structures (hist | edit) [853 bytes] Docs admin (talk | contribs) (Created page with "# Go to '''Sample Libraries > Compounds > Search Compounds''' and click the ‘List Entry’ link. # Paste the list of compounds for which you need activity data. Click the ‘Search’ button. # RxPlora displays the search results and orders the results by the compound IDs in a numerically ascending fashion. # To download the structures, click the export icon. This brings up a new window to download the structures in either an SD file or in a csv file that would include...") Tag: Visual edit
- 19:21, 26 September 2024 Download activity on a list of compounds (hist | edit) [1,376 bytes] Docs admin (talk | contribs) (Created page with "# Select '''Sample Libraries > Compounds > Search Compounds''' Note: If you need to download activity for a list of substances or siRNA, select Sample Libraries > Substances > Search Substances or Sample Libraries > siRNA > Search siRNA respectively. # Click the ‘List Entry’ link. # Paste the numerical list of compounds (without any prefixes such as CCG- or SID-) into the search box. Click the ‘Search’ button. # MScreen reorders the list in numerically ascending...") Tag: Visual edit
- 18:36, 26 September 2024 Curve-fit my CRC plate (hist | edit) [1,561 bytes] Docs admin (talk | contribs) (Created page with " This feature to curve-fit CRC data becomes available once the HTS lab or your lab loads your CRC data into MScreen. The assays that can be curve-fit will not be published until you notify the lab once you are satisfied with your curve-fits. The curve-fitting program uses a non-linear regression program to determine the curve parameters. # Select '''HTS Screens > CRC Screens > Preview and QC''' from the MScreen menu. Navigate to the assay that you would like to curve-fi...") Tag: Visual edit
- 18:35, 26 September 2024 Get a summary report on my target (hist | edit) [331 bytes] Docs admin (talk | contribs) (Created page with "# Select '''HTS Screens > Targets > Target Activity''' Report # Select the target from the target drop-down list and the activity criteria for which you want to get your report, and click the ‘Generate Report’ button. # MScreen displays the target summary report for primary, CRC, and follow-up screens.") Tag: Visual edit
- 18:34, 26 September 2024 Run a Chemical Structure Search (hist | edit) [933 bytes] Docs admin (talk | contribs) (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
- 18:33, 26 September 2024 Upload screening data (hist | edit) [2,367 bytes] Docs admin (talk | contribs) (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
- 18:09, 26 September 2024 Triage My Assay Data (hist | edit) [459 bytes] Docs admin (talk | contribs) (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
- 18:02, 26 September 2024 Reformat 384-well stocks into 1536 wells (hist | edit) [163 bytes] Docs admin (talk | contribs) (Created page with "# Select '''Manage Plates > Reformat Plates''' and click on '''Option 2''' # Follow steps 2 to 5 from the 96-to-384 link") Tag: Visual edit
- 18:01, 26 September 2024 Reformat 96-well stocks into 384 wells (hist | edit) [1,668 bytes] Docs admin (talk | contribs) (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
- 18:00, 26 September 2024 Cherrypick a hitlist for reconfirmation (hist | edit) [1,984 bytes] Docs admin (talk | contribs) (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...") Tag: Visual edit
- 17:58, 26 September 2024 Cherrypick a hitlist for CRC (hist | edit) [2,281 bytes] Docs admin (talk | contribs) (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...") Tag: Visual edit
- 17:55, 26 September 2024 How does MScreen normalize the viability data on siRNA screens (hist | edit) [699 bytes] Docs admin (talk | contribs) (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...")
- 17:53, 26 September 2024 How does MScreen apply value correction to assay data (hist | edit) [507 bytes] Docs admin (talk | contribs) (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
- 17:50, 26 September 2024 What are the different types of chemoinformatics tools available (hist | edit) [257 bytes] Docs admin (talk | contribs) (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]") Tag: Visual edit
- 17:44, 26 September 2024 What are the different types of reports available (hist | edit) [354 bytes] Docs admin (talk | contribs) (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
- 17:41, 26 September 2024 What do the columns in an output file mean (hist | edit) [985 bytes] Docs admin (talk | contribs) (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...")
- 17:38, 26 September 2024 What is Z' (read Z-factor) (hist | edit) [1,232 bytes] Docs admin (talk | contribs) (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...")
- 17:24, 26 September 2024 What do the colors on the plate display mean (hist | edit) [321 bytes] Docs admin (talk | contribs) (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.")
- 17:15, 26 September 2024 What is pic50 or pac50 (hist | edit) [912 bytes] Docs admin (talk | contribs) (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
- 16:22, 26 September 2024 FAQ (hist | edit) [448 bytes] Docs admin (talk | contribs) (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?")
- 16:20, 26 September 2024 Tutorials (hist | edit) [750 bytes] Docs admin (talk | contribs) (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...")
- 14:54, 26 September 2024 Welcome (hist | edit) [2,107 bytes] Docs admin (talk | contribs) (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...")
