diff --git a/lincs/src/org/labkey/lincs/CustomGctBuilder.java b/lincs/src/org/labkey/lincs/CustomGctBuilder.java
index 0e446e66..f6fa8f52 100644
--- a/lincs/src/org/labkey/lincs/CustomGctBuilder.java
+++ b/lincs/src/org/labkey/lincs/CustomGctBuilder.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.lincs;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.util.FileUtil;
 import org.labkey.lincs.view.GctUtils;
 
@@ -34,7 +35,7 @@ public class CustomGctBuilder
 {
     private final String[] multiValueProbeAnnotations = new String[] {"pr_probe_normalization_group", "pr_probe_suitability_manual", "pr_normalization_peptide_id"};
 
-    private final static Logger _log = Logger.getLogger(CustomGctBuilder.class);
+    private final static Logger _log = LogManager.getLogger(CustomGctBuilder.class);
 
     public Gct build(List<Path> files, List<LincsController.SelectedAnnotation> selectedAnnotations,
                      Set<String> ignoredProbeAnnotations, Set<String> ignoredReplicateAnnotations) throws Gct.GctFileException
diff --git a/lincs/src/org/labkey/lincs/DocImportListenter.java b/lincs/src/org/labkey/lincs/DocImportListenter.java
index 0408dd10..8655d502 100644
--- a/lincs/src/org/labkey/lincs/DocImportListenter.java
+++ b/lincs/src/org/labkey/lincs/DocImportListenter.java
@@ -1,6 +1,7 @@
 package org.labkey.lincs;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.exp.api.ExpRun;
@@ -33,7 +34,7 @@
 
 public class DocImportListenter implements ExperimentListener
 {
-    private static Logger _log = Logger.getLogger(DocImportListenter.class);
+    private static Logger _log = LogManager.getLogger(DocImportListenter.class);
 
     @Override
     public void beforeRunCreated(Container container, User user, ExpProtocol protocol, ExpRun run)
diff --git a/lincs/src/org/labkey/lincs/LincsManager.java b/lincs/src/org/labkey/lincs/LincsManager.java
index f76c94ba..b25c2717 100644
--- a/lincs/src/org/labkey/lincs/LincsManager.java
+++ b/lincs/src/org/labkey/lincs/LincsManager.java
@@ -16,7 +16,8 @@
 
 package org.labkey.lincs;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.DbSchemaType;
@@ -48,7 +49,7 @@ public class LincsManager
 {
     private static final LincsManager _instance = new LincsManager();
 
-    private static Logger _log = Logger.getLogger(LincsManager.class);
+    private static Logger _log = LogManager.getLogger(LincsManager.class);
 
     private LincsManager()
     {
diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspTask.java b/lincs/src/org/labkey/lincs/psp/LincsPspTask.java
index 9b369a9d..40ae86ee 100644
--- a/lincs/src/org/labkey/lincs/psp/LincsPspTask.java
+++ b/lincs/src/org/labkey/lincs/psp/LincsPspTask.java
@@ -1,6 +1,7 @@
 package org.labkey.lincs.psp;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.Container;
 import org.labkey.api.module.ModuleLoader;
diff --git a/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java b/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java
index 65d35faa..a81e6a3b 100644
--- a/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java
+++ b/lincs/src/org/labkey/lincs/psp/LincsPspUtil.java
@@ -2,7 +2,8 @@
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.json.JSONObject;
 import org.json.simple.JSONArray;
 import org.json.simple.parser.JSONParser;
diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java
index 7b2325e3..c9647667 100644
--- a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java
+++ b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicController.java
@@ -19,7 +19,8 @@
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.validator.routines.EmailValidator;
 import org.apache.commons.validator.routines.UrlValidator;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.NotNull;
 import org.json.JSONObject;
 import org.labkey.api.action.ApiResponse;
@@ -185,7 +186,7 @@ public PanoramaPublicController()
         setActionResolver(_actionResolver);
     }
 
-    private static final Logger LOG = Logger.getLogger(PanoramaPublicController.class);
+    private static final Logger LOG = LogManager.getLogger(PanoramaPublicController.class);
 
     // ------------------------------------------------------------------------
     // BEGIN Actions for journal groups.
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java
index 93684568..1054be4a 100644
--- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java
+++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java
@@ -15,9 +15,10 @@
  */
 package org.labkey.panoramapublic.pipeline;
 
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.apache.commons.lang3.RandomStringUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
diff --git a/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java b/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java
index b469da5b..474a4a56 100644
--- a/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java
+++ b/panoramapublic/src/org/labkey/panoramapublic/pipeline/ExperimentExportTask.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.panoramapublic.pipeline;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.admin.FolderExportContext;
 import org.labkey.api.admin.FolderWriterImpl;
@@ -109,7 +110,7 @@ public void writeExperiment(CopyExperimentJobSupport support, ExperimentAnnotati
 
         FolderExportContext ctx = new FolderExportContext(user, source, PageFlowUtil.set(templateWriterTypes),
                 null, includeSubfolders, PHI.NotPHI, false,
-                false, false, new StaticLoggerGetter(Logger.getLogger(FolderWriterImpl.class)));
+                false, false, new StaticLoggerGetter(LogManager.getLogger(FolderWriterImpl.class)));
 
 
         File exportDir = support.getExportDir();
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java
index 7e25d86b..1a415f72 100644
--- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java
+++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/ExperimentModificationGetter.java
@@ -16,7 +16,8 @@
 package org.labkey.panoramapublic.proteomexchange;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.data.Container;
@@ -38,7 +39,7 @@
 
 public class ExperimentModificationGetter
 {
-    private static final Logger LOG = Logger.getLogger(ExperimentModificationGetter.class);
+    private static final Logger LOG = LogManager.getLogger(ExperimentModificationGetter.class);
 
     public static List<PxModification> getModifications(ExperimentAnnotations expAnnot)
     {
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java
index cc0a4c41..b1149a0f 100644
--- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java
+++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/NcbiUtils.java
@@ -48,7 +48,7 @@ public class NcbiUtils
     private static final String eutilsUrl = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=taxonomy";
     private static final String autoCompUrl = "https://blast.ncbi.nlm.nih.gov/portal/utils/autocomp.fcgi?dict=taxids_sg&q=";
 
-    // private static final Logger LOG = Logger.getLogger(NcbiUtils.class);
+    // private static final Logger LOG = LogManager.getLogger(NcbiUtils.class);
 
     public static List<JSONObject> getCompletions(String token) throws PxException
     {
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java
index b0b23d81..982c7c24 100644
--- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java
+++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/PxHtmlWriter.java
@@ -16,7 +16,8 @@
 package org.labkey.panoramapublic.proteomexchange;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.security.User;
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.ShortURLRecord;
@@ -33,7 +34,7 @@ public class PxHtmlWriter extends PxWriter
 {
     private final StringBuilder _output;
 
-    private static final Logger LOG = Logger.getLogger(PxHtmlWriter.class);
+    private static final Logger LOG = LogManager.getLogger(PxHtmlWriter.class);
 
     public PxHtmlWriter(StringBuilder out)
     {
diff --git a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/SubmissionDataValidator.java b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/SubmissionDataValidator.java
index 9f6e7de3..3f687121 100644
--- a/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/SubmissionDataValidator.java
+++ b/panoramapublic/src/org/labkey/panoramapublic/proteomexchange/SubmissionDataValidator.java
@@ -17,7 +17,8 @@
 
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.data.CompareType;
@@ -52,7 +53,7 @@ public class SubmissionDataValidator
     public static final int MIN_ABSTRACT_LENGTH = 50;
     public static final int MIN_TITLE_LENGTH = 30;
 
-    private static final Logger LOG = Logger.getLogger(SubmissionDataValidator.class);
+    private static final Logger LOG = LogManager.getLogger(SubmissionDataValidator.class);
 
     public static boolean isValid(ExperimentAnnotations expAnnot)
     {
diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java b/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java
index b5457068..5cb49cbd 100644
--- a/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java
+++ b/panoramapublic/src/org/labkey/panoramapublic/query/JournalManager.java
@@ -15,7 +15,8 @@
  */
 package org.labkey.panoramapublic.query;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.admin.FolderExportPermission;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
@@ -69,7 +70,7 @@
  */
 public class JournalManager
 {
-    private static final Logger LOG = Logger.getLogger(JournalManager.class);
+    private static final Logger LOG = LogManager.getLogger(JournalManager.class);
 
     public static List<Journal> getJournals()
     {
diff --git a/signup/src/org/labkey/signup/SignUpController.java b/signup/src/org/labkey/signup/SignUpController.java
index 75ff2d1d..a0844372 100644
--- a/signup/src/org/labkey/signup/SignUpController.java
+++ b/signup/src/org/labkey/signup/SignUpController.java
@@ -17,7 +17,8 @@
 package org.labkey.signup;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.action.ReadOnlyApiAction;
 import org.labkey.api.action.MutatingApiAction;
 import org.labkey.api.action.ApiResponse;
@@ -66,7 +67,7 @@
 
 public class SignUpController extends SpringActionController
 {
-    private static final Logger _log = Logger.getLogger(SignUpController.class);
+    private static final Logger _log = LogManager.getLogger(SignUpController.class);
 
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(SignUpController.class);
 
diff --git a/signup/src/org/labkey/signup/SignUpListener.java b/signup/src/org/labkey/signup/SignUpListener.java
index 0a684c7a..7062879e 100644
--- a/signup/src/org/labkey/signup/SignUpListener.java
+++ b/signup/src/org/labkey/signup/SignUpListener.java
@@ -16,7 +16,8 @@
 
 package org.labkey.signup;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager.ContainerListener;
@@ -30,7 +31,7 @@
 
 public class SignUpListener implements ContainerListener, UserManager.UserListener
 {
-    private static final Logger _log = Logger.getLogger(SignUpListener.class);
+    private static final Logger _log = LogManager.getLogger(SignUpListener.class);
 
     @Override
     public void userDeletedFromSite(User user)
diff --git a/testresults/src/org/labkey/testresults/SendTestResultsEmail.java b/testresults/src/org/labkey/testresults/SendTestResultsEmail.java
index 8f345e83..0314d56f 100644
--- a/testresults/src/org/labkey/testresults/SendTestResultsEmail.java
+++ b/testresults/src/org/labkey/testresults/SendTestResultsEmail.java
@@ -1,6 +1,7 @@
 package org.labkey.testresults;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.SQLFragment;
@@ -46,7 +47,7 @@ public interface DEFAULT_EMAIL {
         String ADMIN_EMAIL = "yuval@uw.edu";
     }
 
-    private static final Logger LOG = Logger.getLogger(SendTestResultsEmail.class);
+    private static final Logger LOG = LogManager.getLogger(SendTestResultsEmail.class);
 
     public SendTestResultsEmail()
     {
diff --git a/testresults/src/org/labkey/testresults/TestResultsController.java b/testresults/src/org/labkey/testresults/TestResultsController.java
index 83ede95d..6a9de8e4 100644
--- a/testresults/src/org/labkey/testresults/TestResultsController.java
+++ b/testresults/src/org/labkey/testresults/TestResultsController.java
@@ -19,7 +19,8 @@
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.time.DateUtils;
 import org.apache.commons.validator.routines.EmailValidator;
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.action.ApiSimpleResponse;
 import org.labkey.api.action.MutatingApiAction;
@@ -118,7 +119,7 @@
  */
 public class TestResultsController extends SpringActionController
 {
-    private static final Logger _log = Logger.getLogger(TestResultsController.class);
+    private static final Logger _log = LogManager.getLogger(TestResultsController.class);
     private static final SimpleDateFormat MDYFormat = new SimpleDateFormat("MM/dd/yyyy");
 
     private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(TestResultsController.class);