sacdallago bio_embeddings issues

sacdallago / bio_embeddings

Get protein embeddings from protein sequences

http://docs.bioembeddings.com

MIT License

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issues

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Installation error in installing bio embedding package via pip

#247 amalislam675 opened 1 month ago
0
Can't install well to run bio_embed

#246 Lsz-20 opened 2 months ago
1
Not able to run and pip install bioembeddings

#245 rmagesh148 opened 2 months ago
4
Protocol prottrans_t5_bfd: HTTPError: HTTP Error 406: Not Acceptable

#244 jiaming28 opened 4 months ago
0
Can Word2Vec be used for 4, 5 and 6 kmer? If possible, which file I need to changed and which parameter. I am seeking Guidance on Adapting Word2Vec Code for 4kmer Sequences

#243 faruk17035 opened 6 months ago
0
Protocol prottrans_bert_bfd: OSError: Unable to load weights from pytorch checkpoint file for .catch/bio_embeddings/prottrans_bert_bfd/model_directory/pytorch_model.bin' at '.catch/bio_embeddings/prottrans_bert_bfd/model_directory/pytorch_model.bin'. If you tried to load a PyTorch model from a TF 2.0 checkpoint, please set from_tf=True.

#242 Meng-AnunaAI opened 7 months ago
0
Cannot Import Any Embedder "load()" has been removed, use yaml = YAML(typ='rt') yaml.load(...)

#241 wijuliano opened 7 months ago
0
Protocol esm1b: AttributeError: 'dict' object has no attribute 'startswith'

#240 dvonkan opened 9 months ago
0
from where comes the models in "bio_embeddings/utilities /defaults.yml", where is docs, parameters, dataset ?

#239 laraque opened 10 months ago
0
Protocol prottrans_t5_xl_u50: PermissionError: [Errno 13] Permission denied: 'C:\\Users\\user\\AppData\\Local\\Temp\\tmpk7e1m0jg'

#238 jbattjes opened 12 months ago
1
Tensor size issue

#237 J-JEMINA closed 11 months ago
0
Cant install bio_embeddings in colab

#236 IliasGewr opened 1 year ago
3
AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'

#235 VarianZhou opened 1 year ago
0
3D Protein Embeddings

#234 ChatterjeeAyan opened 1 year ago
0
Error during first step - greenlet size changed, may indicate binary incompatibility.

#233 igwill opened 1 year ago
1
Hard times trying to run the bindEmbed21 example.

#232 Ravy-LFL opened 1 year ago
0
Can not install bioembedings on ubuntu? Please help

#231 faruk17035 opened 1 year ago
1
Can not install bio-embedding in wsl

#230 faruk17035 opened 1 year ago
2
Bump werkzeug from 2.0.3 to 2.2.3

#229 dependabot[bot] opened 1 year ago
0
Docker containers shutting down within a few seconds of starting

#228 kthurimella opened 1 year ago
0
Bump ipython from 8.4.0 to 8.10.0

#227 dependabot[bot] opened 1 year ago
0
Bump oauthlib from 3.2.0 to 3.2.2

#226 dependabot[bot] opened 1 year ago
0
Custom embeddings

#225 rhysnewell opened 1 year ago
0
OSError: Unable to open file (truncated file: eof = 63504384, sblock->base_addr = 0, stored_eof = 374434776)

#224 gerdos opened 1 year ago
1
Protocol prottrans_t5_xl_u50: URLError: <urlopen error [Errno 113] No route to host>

#223 Azai-yx opened 1 year ago
1
Allow torch up to next major version

#222 ecederstrand opened 1 year ago
1
Bump certifi from 2022.6.15 to 2022.12.7

#221 dependabot[bot] opened 1 year ago
0
Bump pillow from 9.1.1 to 9.3.0

#220 dependabot[bot] opened 1 year ago
0
Update jax-unirep dependency version

#219 fedorn opened 1 year ago
0
Add support for ESM-2 and ESMFold

#218 fedorn opened 1 year ago
3
CUDA out of memory.

#217 wenyuhaokikika opened 1 year ago
2
I want to know the configuration of the people who run successfully

#216 sudo349 opened 1 year ago
2
AssertionError: Failed in nopython mode pipeline (step: native lowering) Storing i64 to ptr of i32 ('dim'). FE type int32

#215 sudo349 opened 1 year ago
0
It may be better to let the user define whether the same redundant is allowed or not

#212 wenyuhaokikika closed 1 year ago
1
segmentation fault

#211 yangyangdotcom opened 1 year ago
1
Feature Request: Add Worker version to status API

#210 t03i opened 1 year ago
0
Bump joblib from 1.1.0 to 1.2.0

#209 dependabot[bot] opened 1 year ago
0
Bump protobuf from 3.19.4 to 3.19.5

#208 dependabot[bot] opened 1 year ago
0
Bump oauthlib from 3.2.0 to 3.2.1

#207 dependabot[bot] closed 1 year ago
1
Bump mako from 1.2.1 to 1.2.2

#206 dependabot[bot] opened 1 year ago
0
Package dependency error.

#205 DimitrisAlivas opened 1 year ago
3
Protocol esm: UnpicklingError: invalid load key, '<'.

#204 wenyuhaokikika closed 2 years ago
1
Protocol deepblast: AttributeError: can't set attribute

#203 XiaofangJ closed 1 year ago
0
Text on embed.predictprotein.org

#202 C-Marquet closed 1 year ago
1
render_3D_scatter_plotly Error

#201 drorhunvural opened 2 years ago
0
ImportError when importing ProtTransT5XLU50Embedder

#200 AugustEhl opened 2 years ago
1
detokenize/reverse embedded array

#199 drorhunvural opened 2 years ago
1
Bump notebook from 6.4.3 to 6.4.12

#198 dependabot[bot] closed 2 years ago
1
webserver worker failing on no flask?

#197 sacdallago closed 2 years ago
1
How to solve this error?

#196 faruk17035 closed 2 years ago
2