Tweet
What happen to Ensembl biomart website?
I just can not download the result file. It shows network error when I download something. Sometimes it sucess sometimes it fail. Anyone knows?
-
-
To me, it happens quite often... Just try again in a while... -
Try in the different time of the day/weekend also try develop your ovn error handling
As far, as I remember, some bits of the ensembl used to be hosted on the amazon...
While cloud has some advantages, the correct configuration of these services (supply/demand side management is also extremelly important)...
Othervice it looks like there was not adequate provisioning, when the demant went up or some internet link to their server simply got overloaded...
Another problem is the lack of proper error handling in dome bioperl/biopyhon modules, when the data retrieval error just aborts the whole program instead of returning some error status, so the main program can handle it.
So to overcome the reality of the internet based environment one needs either:
1. If data needed once - make a resilient pipeline, which does data retival as a separate process for each request, and saves the results to separate file on the disk. Then the master process checks the batch, and retries the broken parts.
2. If data needed constantly - than decide which databases are needed, download mysql dump(s) from the ftp.ensembl.org/pub ftp site and setup a local mysql mirror.
Than use DBI/Mysql to query the db(s).Comment
-
Yeah, I think it just a random error but for big download, the error quite often. As for my need, I just occacionally need some data but probably I will try to download the mysql because I only need human database and it quite specific.Comment
-
If you don't want to deal with MySQL then you can use FTP directly as pointed by @Markiyan: ftp://ftp.ensembl.org/pub/release-83.../homo_sapiens/ Look for the latest release-NN directory.Comment
-
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...04-04-2024, 04:25 PM -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM
Comment