diff --git a/MODULE.bazel b/MODULE.bazel
index a4172b329..c99b93222 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -4,7 +4,7 @@ pyrovelocity MODULE
 
 module(
     name = "pyrovelocity",
-    version = "0.3.0",
+    version = "0.4.0b1",
     compatibility_level = 1,
 )
 
diff --git a/Makefile b/Makefile
index cdb06bc97..f3a84b06f 100644
--- a/Makefile
+++ b/Makefile
@@ -913,8 +913,8 @@ approve-prs: ## Approve github pull requests from bots: PR_ENTRIES="2-5 10 12-18
 		fi; \
 	done
 
-PREVIOUS_VERSION := 0.3.0b7
-NEXT_VERSION := 0.3.0
+PREVIOUS_VERSION := 0.3.0
+NEXT_VERSION := 0.4.0b1
 VERSION_FILES := \
 	pyproject.toml \
 	conda/colab/construct.yaml \
diff --git a/conda/colab/construct.yaml b/conda/colab/construct.yaml
index 772ff1e43..62694b7c9 100644
--- a/conda/colab/construct.yaml
+++ b/conda/colab/construct.yaml
@@ -1,5 +1,5 @@
 name: pyrovelocity-colab
-version: 0.3.0
+version: 0.4.0b1
 
 channels:
   - pytorch
@@ -268,7 +268,7 @@ specs:
   - jsonschema-specifications=2023.12.1=pyhd8ed1ab_0
   - jupyter_client=8.6.2=pyhd8ed1ab_0
   - jupyter_core=5.7.2=py311h38be061_0
-  - jupyterlab_pygments=0.3.0=pyhd8ed1ab_1
+  - jupyterlab_pygments=0.4.0b1=pyhd8ed1ab_1
   - jupyterlab_widgets=3.0.11=pyhd8ed1ab_0
   - jupytext=1.16.4=pyh80e38bb_0
   - kernel-headers_linux-64=3.10.0=h4a8ded7_16
@@ -344,7 +344,7 @@ specs:
   - libparquet=15.0.2=hfd5bfe4_19_cpu
   - libpng=1.6.43=h2797004_0
   - libprotobuf=4.25.3=h08a7969_0
-  - libre2-11=2023.09.01=h5a48ba9_2
+  - libre2-11=20.4.0b19.01=h5a48ba9_2
   - librsvg=2.58.2=h9564881_1
   - libsanitizer=12.4.0=h46f95d5_0
   - libsecret=0.18.8=h329b89f_2
@@ -396,7 +396,7 @@ specs:
   - msal=1.30.0=pyhd8ed1ab_0
   - msal_extensions=1.1.0=py311h38be061_1
   - msgpack-python=1.0.8=py311h52f7536_0
-  - mudata=0.3.0=pyhd8ed1ab_0
+  - mudata=0.4.0b1=pyhd8ed1ab_0
   - multidict=6.0.5=py311h459d7ec_0
   - multipledispatch=0.6.0=pyhd8ed1ab_1
   - munkres=1.1.4=pyh9f0ad1d_0
@@ -526,7 +526,7 @@ specs:
   - rapidfuzz=3.9.6=py311hf86e51f_0
   - rav1e=0.6.6=he8a937b_2
   - rdma-core=53.0=he02047a_0
-  - re2=2023.09.01=h7f4b329_2
+  - re2=20.4.0b19.01=h7f4b329_2
   - readchar=4.2.0=pyhd8ed1ab_0
   - readline=8.2=h8228510_1
   - referencing=0.35.1=pyhd8ed1ab_0
@@ -604,7 +604,7 @@ specs:
   - typing-extensions=4.12.2=hd8ed1ab_0
   - typing_extensions=4.12.2=pyha770c72_0
   - typing_inspect=0.9.0=pyhd8ed1ab_0
-  - tzdata=2024a=h0c530f3_0
+  - tzdata=2024a=h0c530.4.0b1
   - ucx=1.16.0=h1e563ba_5
   - umap-learn=0.5.6=py311h38be061_0
   - uritemplate=4.1.1=pyhd8ed1ab_0
diff --git a/containers/gpu.Dockerfile b/containers/gpu.Dockerfile
index b271571d5..ab7111c6d 100644
--- a/containers/gpu.Dockerfile
+++ b/containers/gpu.Dockerfile
@@ -77,7 +77,7 @@ COPY . /root
 # development
 RUN pip install --no-deps -e .
 # distribution
-# RUN pip install pyrovelocity==0.3.0
+# RUN pip install pyrovelocity==0.4.0b1
 
 ARG tag
 ENV FLYTE_INTERNAL_IMAGE $tag
diff --git a/containers/pkg.Dockerfile b/containers/pkg.Dockerfile
index cb7e071e2..c81f3c81d 100644
--- a/containers/pkg.Dockerfile
+++ b/containers/pkg.Dockerfile
@@ -34,7 +34,7 @@ COPY . /root
 # development
 RUN pip install --no-deps -e .
 # distribution
-# RUN pip install pyrovelocity==0.3.0
+# RUN pip install pyrovelocity==0.4.0b1
 
 ARG tag
 ENV FLYTE_INTERNAL_IMAGE $tag
diff --git a/docs/source/notebooks/pyrovelocity_colab_template.ipynb b/docs/source/notebooks/pyrovelocity_colab_template.ipynb
index cde05e50f..5d41f8678 100644
--- a/docs/source/notebooks/pyrovelocity_colab_template.ipynb
+++ b/docs/source/notebooks/pyrovelocity_colab_template.ipynb
@@ -70,7 +70,7 @@
         }
       ],
       "source": [
-        "pyrovelocity_version = \"0.3.0\"\n",
+        "pyrovelocity_version = \"0.4.0b1\"\n",
         "pyrovelocity_colab_script_url = (\n",
         "    \"https://storage.googleapis.com/pyrovelocity/data/scripts/\"\n",
         "    + f\"pyrovelocity-colab-{pyrovelocity_version}-Linux-x86_64.sh\"\n",
diff --git a/pyproject.toml b/pyproject.toml
index 2eb53ff42..520193669 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyrovelocity"
-version = "0.3.0"
+version = "0.4.0b1"
 packages = [{ include = "pyrovelocity", from = "src" }]
 description = "A multivariate RNA Velocity model to estimate future cell states with uncertainty using probabilistic modeling with pyro."
 authors = ["pyrovelocity team"]
diff --git a/scripts/conda b/scripts/conda
index 42d65e655..1e769b676 100755
--- a/scripts/conda
+++ b/scripts/conda
@@ -3,7 +3,7 @@
 set -euo pipefail
 
 PACKAGE_NAME="pyrovelocity"
-PACKAGE_VERSION="0.3.0"
+PACKAGE_VERSION="0.4.0b1"
 CONDA_BUILD_STRING="pyhff70e4c"
 CONDA_BUILD_NUMBER="0"
 # CONDA_CHANNEL_LABEL="pyrovelocity_dev"
@@ -32,7 +32,7 @@ Example:
 
     ./conda \\
     --name pyrovelocity \\
-    --version 0.3.0.dev1 \\
+    --version 0.4.0b1.dev1 \\
     --build-string pyhff70e4c \\
     --build-number 0 \\
     --label pyrovelocity_dev
@@ -67,9 +67,9 @@ PACKAGE_SPEC="conda-forge/label/\
 $CONDA_CHANNEL_LABEL::\
 $PACKAGE_NAME=$PACKAGE_VERSION=$CONDA_BUILD_STRING"_"$CONDA_BUILD_NUMBER"
 
-BLUE="\033[0;34;1m"
+BLUE="\0.4.0b1;34;1m"
 BOLD="\033[1m"
-NO_COLOR="\033[0m"
+NO_COLOR="\0.4.0b1m"
 if [ "$USE_COLOR" = false ]; then
     BLUE=""
     BOLD=""