Recently, I rediscovered BioVinci software and I am interested in learning more about it. However, during the past few days, I have sent BioVinci and BioTuring several inquiries via email but I have not yet received any replies. Does anyone here know if the software is still being actively developed?
Dear Rudy,
Did you get any response from the Biovinci team?
Cheers-Kh
Khadijeh Alinezhad : I was about to answer my own question when I saw your follow-up question. Yes, I sent a question to the parent company, BioTuring, and they replied today. Unfortunately, they said that they are currently not supporting BioVinci in order to focus on other products. However, they also said that they hoped to resume the development of BioVinci soon, at which time they would notify users.
At present, my main interest in BioVinci was their implementation of UMAP as a dimension-reduction algorithm, which made the procedure quite easy to use. However, all UMAP software that I have looked at thus far uses the python package, "umap-learn", and I think it would be good to learn how to use this technique directly in order to begin to understand the rationale for tuning the various parameters.
McInnes, L, Healy, J, UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction, ArXiv e-prints 1802.03426, 2018
McInnes, L, Healy, J, Melville, J: UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction, https://arxiv.org/pdf/1802.03426v3.pdf, 2020
https://umap-learn.readthedocs.io/en/latest/index.html
In addition, I mostly use Linux (Linux Mint 20.3 Xfce) as my OS, and of course, python is cross-platform.
Some other software that has UMAP capabilities includes the following:
Eigenvector PLS_Toolbox (commercial; Matlab add-on or "Solo" for standalone; Linux, Mac, Windows)
JMP Pro (commercial; Add-on; requires R; Mac, Windows)
Matlab (commercial; Linux, Mac, Windows)
PAST (free; Mac, Windows)
R (free; Linux, Mac, Windows)
SUMO (free; Windows)
Although UMAP looks quite promising as a dimension-reduction method, it should not be regarded as a panacea, and there are pros and cons to consider (see original preprints cited above as well as the following):
https://www.learndatasci.com/tutorials/applied-dimensionality-reduction-techniques-using-python/
https://cran.r-project.org/web/packages/umap/vignettes/umap.html
Thanks, to complete the software aforementioned I'd all Origin as well.
I was looking for software to do PCA, then I came to Biovinci but unfortunately, because it was just the free rail and couldn't upgrade it, I decided to use origin which I don't have any idea how does it work and am just playing around to figure out how it does.
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