Tjian - Darzacq lab issueshttps://gitlab.com/groups/tjian-darzacq-lab/-/issues2023-06-15T12:27:47Zhttps://gitlab.com/tjian-darzacq-lab/Spot-On-cli/-/issues/2Issue Regarding Usage2023-06-15T12:27:47ZApratim MukherjeeIssue Regarding UsageHi - thank you for uploading this package! I am trying to use the python version but the the Usage section in the ReadMe is currently blank. Could you kindly provide some input regarding this, especially what exact format is required for...Hi - thank you for uploading this package! I am trying to use the python version but the the Usage section in the ReadMe is currently blank. Could you kindly provide some input regarding this, especially what exact format is required for the input files (I currently have tracked single molecule files as .csv)
Thanks!https://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/177Admin panel is unreacheable2021-06-03T09:59:11ZRoyal KittenAdmin panel is unreacheablehttps://spoton.berkeley.edu/admin/SPTGUI/analysis/https://spoton.berkeley.edu/admin/SPTGUI/analysis/https://gitlab.com/tjian-darzacq-lab/covid19_review/-/issues/1Abbott Alere ID NOW and Bhadra ... Ellington OSD-LAMP method2020-04-29T00:49:14ZShyam SaladiAbbott Alere ID NOW and Bhadra ... Ellington OSD-LAMP methodGreat and very timely review. Nice to see it under version control too.
I was under the impression that the ID NOW PoC system was direct swab-to-reaction, in a sense extraction-free. Table S1 C16 suggests extraction is required. It loo...Great and very timely review. Nice to see it under version control too.
I was under the impression that the ID NOW PoC system was direct swab-to-reaction, in a sense extraction-free. Table S1 C16 suggests extraction is required. It looks like Abbott is amending their EUA to actually exclude UTM/VTM eluted samples (link to "ID NOW COVID-19 Technical Brief April 2020" on this page: https://www.alere.com/en/home/product-details/id-now-covid-19.html). Haven't looked to check if the LoD reported in the FDA EUA docs is from VTM/UTM or direct swab samples.
Might also be worth discussing the Bhadra ... Ellington's LAMP-OSD method that improves the LAMP sensitivity and specificity in a neat way: https://www.biorxiv.org/content/10.1101/2020.04.13.039941v1.full.pdfhttps://gitlab.com/tjian-darzacq-lab/Spot-On-TrackMate/-/issues/1Problem uploading2019-03-28T17:20:25ZAndrey AristovProblem uploadingI've installed the plugin and dependencies, but didn't manage to upload to SpotOn at the end of TrackMate with the following error.
```
Converting the tracks to simple XML format.
Preparing XML data.
Connecting to Spot-On:https://spo...I've installed the plugin and dependencies, but didn't manage to upload to SpotOn at the end of TrackMate with the following error.
```
Converting the tracks to simple XML format.
Preparing XML data.
Connecting to Spot-On:https://spoton.berkeley.edu/SPTGUI/uploadapi/
Connection established
Uploading file.
Progress: 100,00%
Could not establish connection with the Spot-On server
The server said:
Misformed request[TIRF_movie_561_50mW_405_skip200_1_MMStack_Pos0.ome-1.xml]
```
I attach the Trackmate-saved xml.
[TIRF_movie_561_50mW_405_skip200_1_MMStack_Pos0.ome-1.xml](/uploads/1c15135e0064c1bbdeaf1a986ab56bf2/TIRF_movie_561_50mW_405_skip200_1_MMStack_Pos0.ome-1.xml)https://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/173dZ correction issue2021-03-31T14:51:30ZAnders dZ correction issueHi Maxime, this is from Xiaona's email:
We tried to check “No” for dZ correction, but this froze the online Spot-on and it could not finish the fitting. Is this a universal issue or just our internet browser?Hi Maxime, this is from Xiaona's email:
We tried to check “No” for dZ correction, but this froze the online Spot-on and it could not finish the fitting. Is this a universal issue or just our internet browser?Royal KittenRoyal Kittenhttps://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/167Buffer overflow when uploading a file with a high number of frames.2017-10-17T16:14:35ZRoyal KittenBuffer overflow when uploading a file with a high number of frames.https://gitlab.com/tjian-darzacq-lab/Spot-On/-/issues/166Spot-On website does not work well in Internet Explorer2017-10-13T01:53:55ZAnders Spot-On website does not work well in Internet ExplorerHi Maxime,
I walked Meagan through Spot-On on her Windows desktop. The drag-n-drop of MAT-files worked in Google Chrome, but not in Internet Explorer. Maybe you can try it out on her computer to get details of the bug.Hi Maxime,
I walked Meagan through Spot-On on her Windows desktop. The drag-n-drop of MAT-files worked in Google Chrome, but not in Internet Explorer. Maybe you can try it out on her computer to get details of the bug.https://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/12Tests are broken2017-08-30T03:25:41ZRoyal KittenTests are brokenSince the software has been repackaged, tests are broken.Since the software has been repackaged, tests are broken.https://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/10`RDP` partitions are not implemented2017-08-30T03:25:41ZRoyal Kitten`RDP` partitions are not implementedhttps://gitlab.com/tjian-darzacq-lab/pySPIRAL-TAP/-/issues/9`demo==3` is not implemented2017-08-30T03:25:41ZRoyal Kitten`demo==3` is not implementedThe content of demo==3 is not implementedThe content of demo==3 is not implemented