- Cv19caingest - public-lists.sanger.ac.uk

wrong md5 checksum for https://covid19.cog.sanger.ac.uk/submissions/release1/haniffa21.processed.h5ad [EXT]
by Daniil Sarkisyan 23 Apr '21

23 Apr '21

Dear COVID-19 Cell Atlas maintainer, I downloaded haniffa21.processed.h5ad from you website twice as follows $ wget https://covid19.cog.sanger.ac.uk/submissions/release1/haniffa21.processed.h… ) And both times $ md5sum haniffa21.processed.h5ad gave me add2501947c585ea6b6ef7429e4bd9f2 haniffa21.processed.h5ad while you provide md5 checksum 42ad74a77fc289b77cfedb7b287f7e23 Since all other files of COVID-19 PBMC Ncl-Cambridge-UCL release 1.0 matched your md5 checksums perfectly, I suspect you provide wrong checksum for haniffa21.processed.h5ad Best Regards, Daniil Sarkisyan, Bioinformatician Department of Immunology, genetics and pathology, BMC B11:406b mobile: +46 70 885 9883, email: daniil.sarkisyan(a)igp.uu.se När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uu.se_om-2Duu_datas… E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uu.se_en_about-2Duu…

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Re: your data on covid19cellatlas [EXT]
by Jonah Cool 08 Apr '21

08 Apr '21

Hi John, No problem at all and I too am excited to see the data on the covid19atlas, which is an awesome community resource. I'm cc'ing that team here to hopefully help with the modifications that you've pointed out. All good things, Jonah On Tue, Apr 6, 2021 at 11:55 AM Tsang, John (NIH/NIAID) [E] < john.tsang(a)nih.gov> wrote: > Hi Jonah, > > Thanks so much! It has been such a pleasure working with you and Pablo on > this and we are very grateful for your support. Excited that our dataset is > now on the human covid19 atlas site! > > I noticed a couple of minor items that would benefit from small textual > changes if possible: > > 1) title of the dataset -> "Blood PBMCs from COVID-19 patients over time" > would be a better title as most of our patients were not fatal. > > 2) lab name - there are quite a few labs in the Laboratory of Immune > Systems Biology (as it's a department). Easiest to put "Tsang Lab" like the > others would be most consistent. > > Thanks again! > > John. > > > > ------------------------------ > *From:* Jonah Cool <jcool(a)chanzuckerberg.com> > *Sent:* Tuesday, April 6, 2021 2:40 PM > *To:* Tsang, John (NIH/NIAID) [E] <john.tsang(a)nih.gov>; Lau, William > (NIH/NIAID) [E] <lauwill(a)mail.nih.gov> > *Subject:* your data on covid19cellatlas > > John & William, > > Hope all is well and you've been getting lots of positive feedback on the > paper. I wanted to quickly confirm that your data is now available (think > it has been for a few days, actually:)) on the covid19cellatlas site > <https://www.covid19cellatlas.org/index.patient.html> under the "patient" > tab. > > Thanks again for working with us on this and looking forward to connecting > again soon. > > All good things, > > Jonah >

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OEM/ODM Manufacturing support [EXT]
by Star Huang 07 Apr '21

07 Apr '21

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Re: h5 files [EXT]
by Reichenberger, Erin R 18 Mar '21

18 Mar '21

Greetings, Thank you for making the data available for download. I have downloaded some data (https://covid19.cog.sanger.ac.uk/submissions/release1/20200804_NasalSwab_Br…) however I have been unable to open it I get errors like this: Warning: Unknown file type: h5ad Warning: 'assay' not set, setting to 'RNA' Creating h5Seurat file for version 3.1.5.9900 Adding X as data Adding X as counts Error: Cannot find feature names in this H5AD file Execution halted Or this: error #001: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dio.c in H5D__read(): line 551: can't read data class: HDF5 major: Dataset minor: Read failed error #002: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_read(): line 1875: unable to read raw data chunk class: HDF5 major: Low-level I/O minor: Read failed error #003: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Dchunk.c in H5D__chunk_lock(): line 2905: data pipeline read failed class: HDF5 major: Data filters minor: Filter operation failed error #004: c:/msys64/home/Jeroen/hdf5-1.8.16/src/H5Z.c in H5Z_pipeline(): line 1347: required filter 'lzf' is not registered class: HDF5 major: Data filters minor: Read failed There are many message boards that have listed possible solutions, but I have not been able to get any of them to work. Could you provide some guidance as to what programs are used to open/manipulate these files please? Sincerely, Erin

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updated dataset for COVID-19 Cell Atlas [EXT]
by Aldinger, Kimberly 01 Mar '21

01 Mar '21

Hi, I previously contributed data to the COVID-19 Cell Atlas. I now have an updated/finalized Fetal Cerebellum dataset that I would like to replace for the dataset that is currently hosted: https://www.covid19cellatlas.org/index.healthy.html What is the best way to transfer the updated .rds? Thanks! Kimberly A Aldinger, PhD (she/her) Center for Integrative Brain Research (CIBR) Seattle Children's Research Institute Member, Brotman Baty Institute for Precision Medicine 206-884-1226 OFFICE 206-884-1210 FAX OFFICE Center for Integrative Brain Research, Seattle Children's Research Institute, 1900 9th Avenue, Seattle, WA 98101 MAIL 1900 9th Avenue, M/S JMB-10, Seattle, WA 98101 WWW https://urldefense.proofpoint.com/v2/url?u=https-3A__www.seattlechildrens.o… CONFIDENTIALITY NOTICE: This e-mail, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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Updating Data on COVID19 Cell Atlas [EXT]
by Carly Ziegler 19 Feb '21

19 Feb '21

Hi Ni and COVID-19 Cell Atlas Team, I hope you are doing well. I'm writing to request some guidance on updating our group's previous submission to the COVID-19 Cell Atlas Portal (current data and viewer is "Nasal Epithelia": https://urldefense.proofpoint.com/v2/url?u=https-3A__cellxgene.cziscience.c… ) We just submitted our manuscript and are in the process of uploading this manuscript as a preprint to biorxiv. We would love to supply the data link for the expanded and updated object. How would you like us to proceed? I can provide an updated h5ad, though I had some difficulties in formatting this properly before (I generally work in R/Seurat). Thanks in advance! Carly -- Carly G. K. Ziegler Harvard/MIT MD-PhD Program Carly_Ziegler(a)hms.harvard.edu carly.ziegler(a)gmail.com 404-375-8912

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The best translation partner you could trust [EXT]
by Yuki Gao 10 Feb '21

10 Feb '21

Dear friend, Hope you are doing well! Following on my previous email, as they tend to slip through the cracks, I wanted to see if you’re looking to expand your business globally? We provide Translation and Localization in 200 languages & 20 industries: Data collection and analysis Language translation Llocalization (software / website / mobile app) Interpretation Transcription Voiceover and dubbing Subtitling Transcreation and copywriting Website development / web design / WordPress WPML MTPE Moreover, we are more than happy to offer you a no-cost 500 words of translation and only ask you to move forward with us if you are impressed by our work. Would it be helpful if we schedule 15-20 minutes, to discuss how can we help you to achieve your goals? Thank you so much! Best regards, Yuki

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Trouble shooting dataset download [EXT]
by Hicks, Sawyer M 05 Feb '21

05 Feb '21

Hello, I am having trouble downloading single cell expression data from your website. After following the download link below, https://covid19.cog.sanger.ac.uk/byrd20_gingiva.processed.h5ad I am brought to a page stating: AccessDeniedcovid19tx0000000000000145d590a-00601c602e-2b1cd989-default2b1cd989-default-default Could you recommend a solution for me? Thank you in advance, Sawyer Hicks Berglund Lab PhD Student

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Data Upload [EXT]
by Emily Stephenson 12 Jan '21

12 Jan '21

Good Morning, If it is possible, we would like to upload our COVID-19 patient data to the COVID-19 Cell Atlas web portal. Please let us know how we can begin this process. The data is currently unpublished. Many thanks and best wishes, Emily Emily Stephenson Haniffa Lab M3.121 Leech Building Faculty of Medical Sciences Newcastle University NE2 4HH Happy New Year

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Application to access your data source [EXT]
by Peng, Dungeng 29 Dec '20

29 Dec '20

Hi, Dear Dr. Sungnak and Covid-cell Atlas I wonder if I could get access to this precious data and I am interested with ACE2 and other gene expressed in kidney epithelial cells. Many thanks! Happy New Year! Dungeng

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