diff --git a/.github/workflows/lint_test.yml b/.github/workflows/lint_test.yml
index 4cf0e4e3..43e2a9f6 100644
--- a/.github/workflows/lint_test.yml
+++ b/.github/workflows/lint_test.yml
@@ -8,7 +8,7 @@ jobs:
       uses: actions/checkout@v2
     - uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Install flake8
       run: pip install flake8
     - name: Flake8
@@ -33,7 +33,7 @@ jobs:
       uses: actions/checkout@v2
     - uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Update apt cache
       run: sudo apt-get update
     - name: Install python-ldap deps
diff --git a/Makefile b/Makefile
index df001475..49b82e52 100644
--- a/Makefile
+++ b/Makefile
@@ -106,9 +106,9 @@ serve-askomics: check-venv build-config create-user
 	@echo 'Serving AskOmics...'
 	. $(ACTIVATE)
 ifeq ($(MODE), dev)
-	FLASK_ENV=development FLASK_APP=app flask run --host=$(HOST) --port $(PORT)
+	FLASK_DEBUG=development FLASK_APP=app flask run --host=$(HOST) --port $(PORT)
 else
-	FLASK_ENV=production FLASK_APP=app gunicorn --timeout $(TIMEOUT) -w $(WORKERS) -b $(HOST):$(PORT) app
+	FLASK_APP=app gunicorn --timeout $(TIMEOUT) -w $(WORKERS) -b $(HOST):$(PORT) app
 endif
 
 serve-celery: check-venv build-config create-user
diff --git a/Pipfile b/Pipfile
index 07dc5e69..dded8ca7 100644
--- a/Pipfile
+++ b/Pipfile
@@ -4,21 +4,20 @@ verify_ssl = true
 name = "pypi"
 
 [packages]
-werkzeug = "==0.16.1"
-flask = "<2"
-flask-reverse-proxy-fix = "*"
+werkzeug = "*"
+flask = "<3"
 validate-email = "*"
 gunicorn = "*"
 python-magic = "*"
 rdflib = "*"
 sparqlwrapper = "*"
 requests = "*"
-celery = "==5.0.5"
+celery = "*"
 redis = "*"
 watchdog = "*"
 gitpython = "*"
-biopython = "*"
-bcbio-gff = "*"
+biopython = "==1.81"
+bcbio-gff = "==0.7.0"
 bioblend = "*"
 pysam = "*"
 pybedtools = "*"
@@ -29,7 +28,7 @@ tld = "*"
 argh = "*"
 python-ldap = "*"
 python-dateutil = "*"
-markupsafe = "==2.0.1"
+markupsafe = "*"
 
 [dev-packages]
 pytest = "*"
diff --git a/Pipfile.lock b/Pipfile.lock
index 5c6cb30f..acfbcf87 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "c3e2bf3cd152f0ca24a42d065d9e7d95f660a97f0cf91f61cef82eb45d016e83"
+            "sha256": "87ea7f78195f7eafa076545d3030cb8f15350d94f953cf008282b956dc3b956b"
         },
         "pipfile-spec": 6,
         "requires": {},
@@ -16,96 +16,85 @@
     "default": {
         "aiohttp": {
             "hashes": [
-                "sha256:002f23e6ea8d3dd8d149e569fd580c999232b5fbc601c48d55398fbc2e582e8c",
-                "sha256:01770d8c04bd8db568abb636c1fdd4f7140b284b8b3e0b4584f070180c1e5c62",
-                "sha256:0912ed87fee967940aacc5306d3aa8ba3a459fcd12add0b407081fbefc931e53",
-                "sha256:0cccd1de239afa866e4ce5c789b3032442f19c261c7d8a01183fd956b1935349",
-                "sha256:0fa375b3d34e71ccccf172cab401cd94a72de7a8cc01847a7b3386204093bb47",
-                "sha256:13da35c9ceb847732bf5c6c5781dcf4780e14392e5d3b3c689f6d22f8e15ae31",
-                "sha256:14cd52ccf40006c7a6cd34a0f8663734e5363fd981807173faf3a017e202fec9",
-                "sha256:16d330b3b9db87c3883e565340d292638a878236418b23cc8b9b11a054aaa887",
-                "sha256:1bed815f3dc3d915c5c1e556c397c8667826fbc1b935d95b0ad680787896a358",
-                "sha256:1d84166673694841d8953f0a8d0c90e1087739d24632fe86b1a08819168b4566",
-                "sha256:1f13f60d78224f0dace220d8ab4ef1dbc37115eeeab8c06804fec11bec2bbd07",
-                "sha256:229852e147f44da0241954fc6cb910ba074e597f06789c867cb7fb0621e0ba7a",
-                "sha256:253bf92b744b3170eb4c4ca2fa58f9c4b87aeb1df42f71d4e78815e6e8b73c9e",
-                "sha256:255ba9d6d5ff1a382bb9a578cd563605aa69bec845680e21c44afc2670607a95",
-                "sha256:2817b2f66ca82ee699acd90e05c95e79bbf1dc986abb62b61ec8aaf851e81c93",
-                "sha256:2b8d4e166e600dcfbff51919c7a3789ff6ca8b3ecce16e1d9c96d95dd569eb4c",
-                "sha256:2d5b785c792802e7b275c420d84f3397668e9d49ab1cb52bd916b3b3ffcf09ad",
-                "sha256:3161ce82ab85acd267c8f4b14aa226047a6bee1e4e6adb74b798bd42c6ae1f80",
-                "sha256:33164093be11fcef3ce2571a0dccd9041c9a93fa3bde86569d7b03120d276c6f",
-                "sha256:39a312d0e991690ccc1a61f1e9e42daa519dcc34ad03eb6f826d94c1190190dd",
-                "sha256:3b2ab182fc28e7a81f6c70bfbd829045d9480063f5ab06f6e601a3eddbbd49a0",
-                "sha256:3c68330a59506254b556b99a91857428cab98b2f84061260a67865f7f52899f5",
-                "sha256:3f0e27e5b733803333bb2371249f41cf42bae8884863e8e8965ec69bebe53132",
-                "sha256:3f5c7ce535a1d2429a634310e308fb7d718905487257060e5d4598e29dc17f0b",
-                "sha256:3fd194939b1f764d6bb05490987bfe104287bbf51b8d862261ccf66f48fb4096",
-                "sha256:41bdc2ba359032e36c0e9de5a3bd00d6fb7ea558a6ce6b70acedf0da86458321",
-                "sha256:41d55fc043954cddbbd82503d9cc3f4814a40bcef30b3569bc7b5e34130718c1",
-                "sha256:42c89579f82e49db436b69c938ab3e1559e5a4409eb8639eb4143989bc390f2f",
-                "sha256:45ad816b2c8e3b60b510f30dbd37fe74fd4a772248a52bb021f6fd65dff809b6",
-                "sha256:4ac39027011414dbd3d87f7edb31680e1f430834c8cef029f11c66dad0670aa5",
-                "sha256:4d4cbe4ffa9d05f46a28252efc5941e0462792930caa370a6efaf491f412bc66",
-                "sha256:4fcf3eabd3fd1a5e6092d1242295fa37d0354b2eb2077e6eb670accad78e40e1",
-                "sha256:5d791245a894be071d5ab04bbb4850534261a7d4fd363b094a7b9963e8cdbd31",
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-                "sha256:b04691bc6601ef47c88f0255043df6f570ada1a9ebef99c34bd0b72866c217ae",
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-                "sha256:caf486ac1e689dda3502567eb89ffe02876546599bbf915ec94b1fa424eeffd4",
-                "sha256:ccc360e87341ad47c777f5723f68adbb52b37ab450c8bc3ca9ca1f3e849e5fe2",
-                "sha256:d25036d161c4fe2225d1abff2bd52c34ed0b1099f02c208cd34d8c05729882f0",
-                "sha256:d52d5dc7c6682b720280f9d9db41d36ebe4791622c842e258c9206232251ab2b",
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-                "sha256:d95fc1bf33a9a81469aa760617b5971331cdd74370d1214f0b3109272c0e1e3c",
-                "sha256:de6a1c9f6803b90e20869e6b99c2c18cef5cc691363954c93cb9adeb26d9f3ae",
-                "sha256:e1d8cb0b56b3587c5c01de3bf2f600f186da7e7b5f7353d1bf26a8ddca57f965",
-                "sha256:e2a988a0c673c2e12084f5e6ba3392d76c75ddb8ebc6c7e9ead68248101cd446",
-                "sha256:e3f1e3f1a1751bb62b4a1b7f4e435afcdade6c17a4fd9b9d43607cebd242924a",
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-                "sha256:ebf3fd9f141700b510d4b190094db0ce37ac6361a6806c153c161dc6c041ccda",
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-                "sha256:ec4fd86658c6a8964d75426517dc01cbf840bbf32d055ce64a9e63a40fd7b771",
-                "sha256:efd2fcf7e7b9d7ab16e6b7d54205beded0a9c8566cb30f09c1abe42b4e22bdcb",
-                "sha256:f0f03211fd14a6a0aed2997d4b1c013d49fb7b50eeb9ffdf5e51f23cfe2c77fa",
-                "sha256:f628dbf3c91e12f4d6c8b3f092069567d8eb17814aebba3d7d60c149391aee3a",
-                "sha256:f8ef51e459eb2ad8e7a66c1d6440c808485840ad55ecc3cafefadea47d1b1ba2",
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-                "sha256:fdee8405931b0615220e5ddf8cd7edd8592c606a8e4ca2a00704883c396e4479"
-            ],
-            "markers": "python_version >= '3.6'",
-            "version": "==3.8.6"
+                "sha256:02ab6006ec3c3463b528374c4cdce86434e7b89ad355e7bf29e2f16b46c7dd6f",
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+                "sha256:c7b5d5d64e2a14e35a9240b33b89389e0035e6de8dbb7ffa50d10d8b65c57449",
+                "sha256:c7e939f1ae428a86e4abbb9a7c4732bf4706048818dfd979e5e2839ce0159f23",
+                "sha256:c88a15f272a0ad3d7773cf3a37cc7b7d077cbfc8e331675cf1346e849d97a4e5",
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+            "markers": "python_version >= '3.8'",
+            "version": "==3.9.1"
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         "aiosignal": {
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@@ -117,19 +106,20 @@
         },
         "amqp": {
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-            "version": "==5.1.1"
+            "version": "==5.2.0"
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         "argh": {
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-            "version": "==0.27.2"
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+            "version": "==0.30.5"
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@@ -139,14 +129,6 @@
             "markers": "python_full_version <= '3.11.2'",
             "version": "==4.0.3"
         },
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@@ -165,10 +147,11 @@
         },
         "billiard": {
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-                "sha256:87103ea78fa6ab4d5c751c4909bcff74617d985de7fa8b672cf8618afd5a875b"
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-            "version": "==3.6.4.0"
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+            "version": "==4.2.0"
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@@ -182,6 +165,8 @@
         "biopython": {
             "hashes": [
                 "sha256:11d673698b3d0d6589292ea951fb62cb24ea27d273eca0d08dbbd956690f97f5",
+                "sha256:175fcddc9f22a070aa6db54755d60c4b31090cc39f5f5f4b0a9a5d1ae3b45cd7",
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@@ -198,10 +183,12 @@
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                 "sha256:9ba33244f0eff830beaa7240065bdb5095d96fded6599b76bbb9ddab45cd2bbd",
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                 "sha256:ccd729249fd5f586dd4c2a3507c2ea2456825d7e615e97c07c409c850eaf4594",
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@@ -212,139 +199,132 @@
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@@ -371,125 +351,113 @@
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@@ -722,40 +673,45 @@
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@@ -775,19 +731,19 @@
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@@ -857,11 +813,11 @@
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@@ -872,21 +828,14 @@
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@@ -919,10 +868,10 @@
                 "flask"
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@@ -968,26 +917,35 @@
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@@ -998,11 +956,11 @@
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@@ -1327,22 +1296,14 @@
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@@ -1353,19 +1314,11 @@
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-                "sha256:97383d78eb34da7e1fa37dd273c20ad4320929af65d156e35a5e2d89566d9dfb",
-                "sha256:984d76483eb32f1bcb536dc27e4ad56bba4baa70be32fa87152832cdd9db0833",
-                "sha256:99df47edb6bda1249d3e80fdabb1dab8c08ef3975f69aed437cb69d0a5de1e28",
-                "sha256:9f02365d4e99430a12647f09b6cc8bab61a6564363f313126f775eb4f6ef798e",
-                "sha256:a30e67a65b53ea0a5e62fe23682cfe22712e01f453b95233b25502f7c61cb415",
-                "sha256:ab3ef638ace319fa26553db0624c4699e31a28bb2a835c5faca8f8acf6a5a902",
-                "sha256:aca6377c0cb8a8253e493c6b451565ac77e98c2951c45f913e0b52facdcff83f",
-                "sha256:add36cb2dbb8b736611303cd3bfcee00afd96471b09cda130da3581cbdc56a6d",
-                "sha256:b2f4bf27480f5e5e8ce285a8c8fd176c0b03e93dcc6646477d4630e83440c6a9",
-                "sha256:b7f2d075102dc8c794cbde1947378051c4e5180d52d276987b8d28a3bd58c17d",
-                "sha256:baa1a4e8f868845af802979fcdbf0bb11f94f1cb7ced4c4b8a351bb60d108145",
-                "sha256:be98f628055368795d818ebf93da628541e10b75b41c559fdf36d104c5787066",
-                "sha256:bf5d821ffabf0ef3533c39c518f3357b171a1651c1ff6827325e4489b0e46c3c",
-                "sha256:c47adbc92fc1bb2b3274c4b3a43ae0e4573d9fbff4f54cd484555edbf030baf1",
-                "sha256:cdfba22ea2f0029c9261a4bd07e830a8da012291fbe44dc794e488b6c9bb353a",
-                "sha256:d6c7ebd4e944c85e2c3421e612a7057a2f48d478d79e61800d81468a8d842207",
-                "sha256:d7f9850398e85aba693bb640262d3611788b1f29a79f0c93c565694658f4071f",
-                "sha256:d8446c54dc28c01e5a2dbac5a25f071f6653e6e40f3a8818e8b45d790fe6ef53",
-                "sha256:deb993cacb280823246a026e3b2d81c493c53de6acfd5e6bfe31ab3402bb37dd",
-                "sha256:e0f138900af21926a02425cf736db95be9f4af72ba1bb21453432a07f6082134",
-                "sha256:e9936f0b261d4df76ad22f8fee3ae83b60d7c3e871292cd42f40b81b70afae85",
-                "sha256:f0567c4dc99f264f49fe27da5f735f414c4e7e7dd850cfd8e69f0862d7c74ea9",
-                "sha256:f5653a225f31e113b152e56f154ccbe59eeb1c7487b39b9d9f9cdb58e6c79dc5",
-                "sha256:f826e31d18b516f653fe296d967d700fddad5901ae07c622bb3705955e1faa94",
-                "sha256:f8ba0e8349a38d3001fae7eadded3f6606f0da5d748ee53cc1dab1d6527b9509",
-                "sha256:f9081981fe268bd86831e5c75f7de206ef275defcb82bc70740ae6dc507aee51",
-                "sha256:fa130dd50c57d53368c9d59395cb5526eda596d3ffe36666cd81a44d56e48872"
+                "sha256:05fb21170423db021895e1ea1e1f3ab3adb85d1c2333cbc2310f2a26bc77272e",
+                "sha256:0a4e4a1aff6c7ac4cd55792abf96c915634c2b97e3cc1c7129578aa68ebd754e",
+                "sha256:10bbfe99883db80bdbaff2dcf681dfc6533a614f700da1287707e8a5d78a8431",
+                "sha256:134da1eca9ec0ae528110ccc9e48041e0828d79f24121a1a146161103c76e686",
+                "sha256:14ff806850827afd6b07a5f32bd917fb7f45b046ba40c57abdb636674a8b559c",
+                "sha256:1577735524cdad32f9f694208aa75e422adba74f1baee7551620e43a3141f559",
+                "sha256:1b40069d487e7edb2676d3fbdb2b0829ffa2cd63a2ec26c4938b2d34391b4ecc",
+                "sha256:1b8dd8c3fd14349433c79fa8abeb573a55fc0fdd769133baac1f5e07abf54aeb",
+                "sha256:1f67c7038d560d92149c060157d623c542173016c4babc0c1913cca0564b9939",
+                "sha256:282c2cb35b5b673bbcadb33a585408104df04f14b2d9b01d4c345a3b92861c2c",
+                "sha256:2c1b19b3aaacc6e57b7e25710ff571c24d6c3613a45e905b1fde04d691b98ee0",
+                "sha256:2ef12179d3a291be237280175b542c07a36e7f60718296278d8593d21ca937d4",
+                "sha256:338ae27d6b8745585f87218a3f23f1512dbf52c26c28e322dbe54bcede54ccb9",
+                "sha256:3c0fae6c3be832a0a0473ac912810b2877c8cb9d76ca48de1ed31e1c68386575",
+                "sha256:3fd4abcb888d15a94f32b75d8fd18ee162ca0c064f35b11134be77050296d6ba",
+                "sha256:42de32b22b6b804f42c5d98be4f7e5e977ecdd9ee9b660fda1a3edf03b11792d",
+                "sha256:47d4f1c5f80fc62fdd7777d0d40a2e9dda0a05883ab11374334f6c4de38adffd",
+                "sha256:504b320cd4b7eff6f968eddf81127112db685e81f7e36e75f9f84f0df46041c3",
+                "sha256:525808b8019e36eb524b8c68acdd63a37e75714eac50e988180b169d64480a00",
+                "sha256:56d9f2ecac662ca1611d183feb03a3fa4406469dafe241673d521dd5ae92a155",
+                "sha256:5bbe06f8eeafd38e5d0a4894ffec89378b6c6a625ff57e3028921f8ff59318ac",
+                "sha256:65c1a9bcdadc6c28eecee2c119465aebff8f7a584dd719facdd9e825ec61ab52",
+                "sha256:68e78619a61ecf91e76aa3e6e8e33fc4894a2bebe93410754bd28fce0a8a4f9f",
+                "sha256:69c0f17e9f5a7afdf2cc9fb2d1ce6aabdb3bafb7f38017c0b77862bcec2bbad8",
+                "sha256:6b2b56950d93e41f33b4223ead100ea0fe11f8e6ee5f641eb753ce4b77a7042b",
+                "sha256:715d3562f79d540f251b99ebd6d8baa547118974341db04f5ad06d5ea3eb8007",
+                "sha256:787003c0ddb00500e49a10f2844fac87aa6ce977b90b0feaaf9de23c22508b24",
+                "sha256:7ef3cb2ebbf91e330e3bb937efada0edd9003683db6b57bb108c4001f37a02ea",
+                "sha256:8023faf4e01efadfa183e863fefde0046de576c6f14659e8782065bcece22198",
+                "sha256:8758846a7e80910096950b67071243da3e5a20ed2546e6392603c096778d48e0",
+                "sha256:8afafd99945ead6e075b973fefa56379c5b5c53fd8937dad92c662da5d8fd5ee",
+                "sha256:8c41976a29d078bb235fea9b2ecd3da465df42a562910f9022f1a03107bd02be",
+                "sha256:8e254ae696c88d98da6555f5ace2279cf7cd5b3f52be2b5cf97feafe883b58d2",
+                "sha256:8f9293864fe09b8149f0cc42ce56e3f0e54de883a9de90cd427f191c346eb2e1",
+                "sha256:9402b03f1a1b4dc4c19845e5c749e3ab82d5078d16a2a4c2cd2df62d57bb0707",
+                "sha256:962f82a3086483f5e5f64dbad880d31038b698494799b097bc59c2edf392fce6",
+                "sha256:9aad3c1755095ce347e26488214ef77e0485a3c34a50c5a5e2471dff60b9dd9c",
+                "sha256:9dcdfd0eaf283af041973bff14a2e143b8bd64e069f4c383416ecd79a81aab58",
+                "sha256:aa57bd9cf8ae831a362185ee444e15a93ecb2e344c8e52e4d721ea3ab6ef1823",
+                "sha256:aa7bd130efab1c280bed0f45501b7c8795f9fdbeb02e965371bbef3523627779",
+                "sha256:ab4a0df41e7c16a1392727727e7998a467472d0ad65f3ad5e6e765015df08636",
+                "sha256:ad9e82fb8f09ade1c3e1b996a6337afac2b8b9e365f926f5a61aacc71adc5b3c",
+                "sha256:af598ed32d6ae86f1b747b82783958b1a4ab8f617b06fe68795c7f026abbdcad",
+                "sha256:b076b6226fb84157e3f7c971a47ff3a679d837cf338547532ab866c57930dbee",
+                "sha256:b7ff0f54cb4ff66dd38bebd335a38e2c22c41a8ee45aa608efc890ac3e3931bc",
+                "sha256:bfce63a9e7834b12b87c64d6b155fdd9b3b96191b6bd334bf37db7ff1fe457f2",
+                "sha256:c011a4149cfbcf9f03994ec2edffcb8b1dc2d2aede7ca243746df97a5d41ce48",
+                "sha256:c9c804664ebe8f83a211cace637506669e7890fec1b4195b505c214e50dd4eb7",
+                "sha256:ca379055a47383d02a5400cb0d110cef0a776fc644cda797db0c5696cfd7e18e",
+                "sha256:cb0932dc158471523c9637e807d9bfb93e06a95cbf010f1a38b98623b929ef2b",
+                "sha256:cd0f502fe016460680cd20aaa5a76d241d6f35a1c3350c474bac1273803893fa",
+                "sha256:ceb01949af7121f9fc39f7d27f91be8546f3fb112c608bc4029aef0bab86a2a5",
+                "sha256:d080e0a5eb2529460b30190fcfcc4199bd7f827663f858a226a81bc27beaa97e",
+                "sha256:dd15ff04ffd7e05ffcb7fe79f1b98041b8ea30ae9234aed2a9168b5797c3effb",
+                "sha256:df0be2b576a7abbf737b1575f048c23fb1d769f267ec4358296f31c2479db8f9",
+                "sha256:e09031c87a1e51556fdcb46e5bd4f59dfb743061cf93c4d6831bf894f125eb57",
+                "sha256:e4dd52d80b8c83fdce44e12478ad2e85c64ea965e75d66dbeafb0a3e77308fcc",
+                "sha256:f698de3fd0c4e6972b92290a45bd9b1536bffe8c6759c62471efaa8acb4c37bc",
+                "sha256:fec21693218efe39aa7f8599346e90c705afa52c5b31ae019b2e57e8f6542bb2",
+                "sha256:ffcc3f7c66b5f5b7931a5aa68fc9cecc51e685ef90282f4a82f0f5e9b704ad11"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
-            "version": "==2.0.1"
+            "markers": "python_version >= '3.7'",
+            "version": "==2.1.3"
         },
         "mccabe": {
             "hashes": [
@@ -1485,12 +1429,12 @@
         },
         "mkdocs": {
             "hashes": [
-                "sha256:8e7970a26183487fe2a1041940c6fd03aa0dbe5549e50c3e7194f565cb3c678a",
-                "sha256:f108e7ab5a7ed3e30826dbf82f37638f0d90d11161644616cc4f01a1e2ab3940"
+                "sha256:3b3a78e736b31158d64dbb2f8ba29bd46a379d0c6e324c2246c3bc3d2189cfc1",
+                "sha256:eb7c99214dcb945313ba30426c2451b735992c73c2e10838f76d09e39ff4d0e2"
             ],
             "index": "pypi",
-            "markers": "python_version >= '3.6'",
-            "version": "==1.2.4"
+            "markers": "python_version >= '3.7'",
+            "version": "==1.5.3"
         },
         "packaging": {
             "hashes": [
@@ -1500,38 +1444,54 @@
             "markers": "python_version >= '3.7'",
             "version": "==23.2"
         },
+        "pathspec": {
+            "hashes": [
+                "sha256:a0d503e138a4c123b27490a4f7beda6a01c6f288df0e4a8b79c7eb0dc7b4cc08",
+                "sha256:a482d51503a1ab33b1c67a6c3813a26953dbdc71c31dacaef9a838c4e29f5712"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==0.12.1"
+        },
+        "platformdirs": {
+            "hashes": [
+                "sha256:11c8f37bcca40db96d8144522d925583bdb7a31f7b0e37e3ed4318400a8e2380",
+                "sha256:906d548203468492d432bcb294d4bc2fff751bf84971fbb2c10918cc206ee420"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==4.1.0"
+        },
         "pluggy": {
             "hashes": [
-                "sha256:c2fd55a7d7a3863cba1a013e4e2414658b1d07b6bc57b3919e0c63c9abb99849",
-                "sha256:d12f0c4b579b15f5e054301bb226ee85eeeba08ffec228092f8defbaa3a4c4b3"
+                "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12",
+                "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7"
             ],
-            "markers": "python_version >= '3.7'",
-            "version": "==1.2.0"
+            "markers": "python_version >= '3.8'",
+            "version": "==1.3.0"
         },
         "pycodestyle": {
             "hashes": [
-                "sha256:2c9607871d58c76354b697b42f5d57e1ada7d261c261efac224b664affdc5785",
-                "sha256:d1735fc58b418fd7c5f658d28d943854f8a849b01a5d0a1e6f3f3fdd0166804b"
+                "sha256:41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f",
+                "sha256:44fe31000b2d866f2e41841b18528a505fbd7fef9017b04eff4e2648a0fadc67"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==2.9.1"
+            "markers": "python_version >= '3.8'",
+            "version": "==2.11.1"
         },
         "pyflakes": {
             "hashes": [
-                "sha256:4579f67d887f804e67edb544428f264b7b24f435b263c4614f384135cea553d2",
-                "sha256:491feb020dca48ccc562a8c0cbe8df07ee13078df59813b83959cbdada312ea3"
+                "sha256:4132f6d49cb4dae6819e5379898f2b8cce3c5f23994194c24b77d5da2e36f774",
+                "sha256:a0aae034c444db0071aa077972ba4768d40c830d9539fd45bf4cd3f8f6992efc"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==2.5.0"
+            "markers": "python_version >= '3.8'",
+            "version": "==3.1.0"
         },
         "pytest": {
             "hashes": [
-                "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002",
-                "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"
+                "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac",
+                "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5"
             ],
             "index": "pypi",
             "markers": "python_version >= '3.7'",
-            "version": "==7.4.2"
+            "version": "==7.4.3"
         },
         "pytest-cov": {
             "hashes": [
@@ -1632,29 +1592,13 @@
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2'",
             "version": "==1.16.0"
         },
-        "tomli": {
-            "hashes": [
-                "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc",
-                "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"
-            ],
-            "markers": "python_version < '3.11'",
-            "version": "==2.0.1"
-        },
-        "typing-extensions": {
-            "hashes": [
-                "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36",
-                "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==4.7.1"
-        },
         "urllib3": {
             "hashes": [
-                "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84",
-                "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"
+                "sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3",
+                "sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54"
             ],
-            "markers": "python_version >= '3.6'",
-            "version": "==2.0.7"
+            "markers": "python_version >= '3.8'",
+            "version": "==2.1.0"
         },
         "watchdog": {
             "hashes": [
@@ -1689,14 +1633,6 @@
             "index": "pypi",
             "markers": "python_version >= '3.7'",
             "version": "==3.0.0"
-        },
-        "zipp": {
-            "hashes": [
-                "sha256:112929ad649da941c23de50f356a2b5570c954b65150642bccdd66bf194d224b",
-                "sha256:48904fc76a60e542af151aded95726c1a5c34ed43ab4134b597665c86d7ad556"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==3.15.0"
         }
     }
 }
diff --git a/askomics/app.py b/askomics/app.py
index a2d9050b..3be5faa3 100644
--- a/askomics/app.py
+++ b/askomics/app.py
@@ -7,6 +7,7 @@
 """
 
 import configparser
+import os
 
 from askomics.api.admin import admin_bp
 from askomics.api.auth import auth_bp
@@ -20,14 +21,13 @@
 from askomics.api.results import results_bp
 from askomics.api.galaxy import galaxy_bp
 from askomics.api.ontology import onto_bp
+from askomics.middleware import PrefixMiddleware
 
 from celery import Celery
 from kombu import Exchange, Queue
 
 from flask import Flask
 
-from flask_reverse_proxy_fix.middleware import ReverseProxyPrefixFix
-
 from pkg_resources import get_distribution
 
 import sentry_sdk
@@ -109,14 +109,16 @@ def create_app(config='config/askomics.ini', app_name='askomics', blueprints=Non
         for blueprint in blueprints:
             app.register_blueprint(blueprint)
 
-        if app.config['ENV'] == "production":
+        is_gunicorn = "gunicorn" in os.environ.get("SERVER_SOFTWARE", "")
+
+        if is_gunicorn:
             log_level = 10 if app.config['DEBUG'] else 20
             gunicorn_logger = logging.getLogger('gunicorn.error')
             app.logger.handlers = gunicorn_logger.handlers
             app.logger.setLevel(log_level)
 
     if proxy_path:
-        ReverseProxyPrefixFix(app)
+        app.wsgi_app = PrefixMiddleware(app.wsgi_app, prefix=proxy_path.rstrip("/"))
 
     return app
 
diff --git a/askomics/middleware.py b/askomics/middleware.py
new file mode 100644
index 00000000..0aa9731c
--- /dev/null
+++ b/askomics/middleware.py
@@ -0,0 +1,13 @@
+class PrefixMiddleware(object):
+
+    def __init__(self, app, prefix=''):
+        self.app = app
+        self.prefix = prefix
+
+    def __call__(self, environ, start_response):
+        if self.prefix is not None:
+            environ['SCRIPT_NAME'] = self.prefix
+            path_info = environ['PATH_INFO']
+            if path_info.startswith(self.prefix):
+                environ['PATH_INFO'] = path_info[len(self.prefix):]
+        return self.app(environ, start_response)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 10c4902e..f77343b2 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -1,4 +1,4 @@
-FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.13 AS builder
+FROM quay.io/askomics/flaskomics-base:4.6.0-alpine3.19 AS builder
 MAINTAINER "Xavier Garnier <xavier.garnier@irisa.fr>"
 
 COPY . /askomics
@@ -7,7 +7,7 @@ WORKDIR /askomics
 RUN make clean-config fast-install build
 
 # Final image
-FROM alpine:3.13
+FROM alpine:3.19
 
 WORKDIR /askomics
 RUN apk add --no-cache make python3 bash git libc-dev libstdc++ nodejs-current npm openldap-dev
diff --git a/docker/DockerfileCelery b/docker/DockerfileCelery
index db08157a..7f2754d8 100644
--- a/docker/DockerfileCelery
+++ b/docker/DockerfileCelery
@@ -1,4 +1,4 @@
-FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.13 AS builder
+FROM quay.io/askomics/flaskomics-base:4.6.0-alpine3.19 AS builder
 MAINTAINER "Xavier Garnier <xavier.garnier@irisa.fr>"
 
 COPY . /askomics
@@ -7,7 +7,7 @@ WORKDIR /askomics
 RUN make clean-config fast-install
 
 # Final image
-FROM alpine:3.13
+FROM alpine:3.19
 
 WORKDIR /askomics
 RUN apk add --no-cache make python3 bash git libc-dev libstdc++ openldap-dev