Skip to content

Commit 5a8104b

Browse files
committed
Updated links to colab notebook
1 parent d079309 commit 5a8104b

File tree

2 files changed

+3
-3
lines changed

2 files changed

+3
-3
lines changed

README.md

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -94,7 +94,7 @@ Metapredict can be used in five different ways:
9494
1. As a stand-alone command-line tool (installable via pip - the code in this repository).
9595
2. As a Python library for integrating into your favorite bioinformatics pipeline (installable via pip - the code in this repository).
9696
3. As a web-server for examining disorder predictions on individual sequences found at [https://metapredict.net/](https://metapredict.net/).
97-
4. *NEW as of August 2022:* as a Google Colab notebook for batch-predicting disorder scores for larger numbers of sequences: [**LINK HERE**](https://colab.research.google.com/github/idptools/metapredict/blob/master/colab/metapredict_colab.ipynb). Performance-wise, batch mode can predict the entire yeast proteome in ~1.5 min using the Colab Notebook and much faster if using a local GPU.
97+
4. *NEW as of August 2022:* as a Google Colab notebook for batch-predicting disorder scores for larger numbers of sequences: [**LINK HERE**](https://colab.research.google.com/drive/1UOrOxun9i23XDE8lFo_4I89Tw8P3Z1D-?usp=sharing). Performance-wise, batch mode can predict the entire yeast proteome in ~1.5 min using the Colab Notebook and much faster if using a local GPU.
9898
5. *NEW as of May 2023:* as part of the [ALBATROSS paper](https://www.nature.com/articles/s41592-023-02159-5), we provide a colab notebook for predicting IDRs on a proteome-wide scale [**LINK HERE**](https://colab.research.google.com/github/holehouse-lab/ALBATROSS-colab/blob/main/idrome_constructor/idrome_constructor.ipynb).
9999

100100
## How to cite

docs/getting_started.rst

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@ What is metapredict?
88

99
Our goal in building **metapredict** was to develop a robust, accurate, and high-performance predictor of intrinsic disorder that is also easy to install and use. As such, **metapredict** is implemented in Python and can be installed directly via `pip` (see below).
1010

11-
metapredict is ALSO available via a `webserver for single sequence prediction <http://https://metapredict.net>`__ and `a Google Colab notebook for batch prediction <https://colab.research.google.com/github/idptools/metapredict/blob/master/colab/metapredict_colab.ipynb>`__. However, this documentation here focuses on the Python package which provides both a set of Python library functions and a set of command-line tools.
11+
metapredict is ALSO available via a `webserver for single sequence prediction <http://https://metapredict.net>`__ and `a Google Colab notebook for batch prediction <https://colab.research.google.com/drive/1UOrOxun9i23XDE8lFo_4I89Tw8P3Z1D-?usp=sharing>`__. However, this documentation here focuses on the Python package which provides both a set of Python library functions and a set of command-line tools.
1212

1313

1414
Recent metapredict updates and news
@@ -145,7 +145,7 @@ How does metapredict V2 differ from V2-FF
145145

146146
metapredict V2 and V2-FF are identical in terms of predictions and features, with the major difference being that metapredict V2-FF offers batched predictions. Batched predictions are automatically parallelized on either the CPU or GPU. In addition, we rewrote the metapredict domain decomposition algorithm in C to provide a 10-20x improvement in performance for this step.
147147

148-
We note that V2-FF was released after CAID, so the performance reported there is the V2 network performance. Because metapredict V2-FF is implemented in a `Google Colab notebook for batch prediction <https://colab.research.google.com/github/idptools/metapredict/blob/master/colab/metapredict_colab.ipynb>`__ you don't have to take our word for it that it's fast; just upload a proteome and see for yourself!
148+
We note that V2-FF was released after CAID, so the performance reported there is the V2 network performance. Because metapredict V2-FF is implemented in a `Google Colab notebook for batch prediction <https://colab.research.google.com/drive/1UOrOxun9i23XDE8lFo_4I89Tw8P3Z1D-?usp=sharing>`__ you don't have to take our word for it that it's fast; just upload a proteome and see for yourself! **Note**: The colab notebook has now been updated to V3. However, all 3 metapredict networks are available for use in the notebook!
149149

150150
What is new as far as the disorder prediction in V3?
151151
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

0 commit comments

Comments
 (0)