34 thoughts on “Feedback”

    1. Hi,
      Please, give me more details what you did to get ORFs then I can help you. Maybe you didn’t set up the size of minimal ORF in the corresponding textfield ? Without this value the app cannot search for ORFs. Also, the search will be perform if user selects the region of search in the sequence.
      Best regards

      Like

      Reply

  2. Hello,

    I am considering to purchase BiolabDonkey. I do a lot of cloning experiments. Can this software be used to perform insilico cloning, restriction digestion, and ligation reactions? Let me know.
    Thank You

    Like

    Reply

    1. Hello Krishna Kurthkoti,
      In BioLabDonkey you can perform a restriction analysis – find positions of restriction sites (present, not present, number of cuts) in a real DNA sequence. If you mean as insilco cloning a graphical representation of cloning scheme of your insert into a vector like in SnapGene program, BioLabDonkey is not providing such functionality. In BioLabDonkey you should copy/paste your insert sequence into a vector sequence in the corresponding restriction sites. BioLabDonkey provides a virtual DNA gel of digested DNA fragment for the restrictases you selected. In BioLabDonkey you can also calculate amounts of insertion and vector needed for a ligation reaction for different insertion/vector ratios.
      If you have further questions, let me know.
      Best regards,
      Valeriy

      Like

      Reply

  3. Thanks for the clarification Valeriy. Are you considering adding such functionality in future releases?

    Like

    Reply

    1. Hi Krishna Kurthkoti,
      Before switching to program developing, I have spent more than 20 year in molecular biology wet lab doing a lot of cloning and, IMO, I see usage of such a graphical cloning not good for the professional education. Dealing with a DNA sequence directly gives you solid skills while a graphical cloning is too superficial. So, the implementation of such a functionality has lowest priority, not for near future.
      Best regards,
      Valeriy

      Like

      Reply

  4. I just purchased the BioLabDonkey and it crashed instantly when I tried to open a file (.dna file, created by SnapGene). I tried a second file, crashed, tried a third file, crashed again. Every time I sent the crash report to Apple. What is going on? Brand new Macbook pro, OS10.15.6, 16g RAM.

    Like

    Reply

    1. Hi,
      I don’t have any crash report from Apple! Please, send me to my e-mail box a crash report and a file (if it is possible) you have tried to open, that I can fix the issue as soon as possible!

      When I had made the function to open SnapGene .dna files, I have tested original SnapGene .dna files dowloaded from official SnapGene website – Basic Cloning Vectros – https://www.snapgene.com/resources/plasmid-files/?set=basic_cloning_vectors. I can open all of them without any problem. What kind of SnapGene .dna files you are trying to open ?

      Best regards,
      Valeriy

      Like

      Reply

      1. Hi Valeriy, I reported that BioLabDonkey crashes every time when I tried to open .dna file. I have sent you an email including the crash report and some .dna files that always lead to crash. Thank you!

        Like

  5. Dear Users, please pay attention if you are trying to open a .dna file from SnapGene. You can have a problem if this file doesn’t have a date of creation in the note section. This issue will be fixed soon in a next update.

    Like

    Reply

  6. I want to contig with two ab1 files. In the sequence columns, when I select unclear region (such as NNN), if the chromatogram data are automatically pop-uped and confirm the peal data, it is easy to confirm and modified and change the sequence. I significantly asked you to update like this.

    Like

    Reply

  7. I have been serial cloner user until Apple decided to stop 32-bit programs. Do you offer the capabilities to do virtual PCR, Gateway/recombination cloning? Not having a trial version is such a bummer, can’t just purchase a software that does not have extensive documentation/user base without having tried it. Thank you for your work though!

    Like

    Reply

  8. Hi. I just got the BioIllustrator app mainly for making plasmid maps. I tried it with a 5000 bp sequence and when I click on the “Plasmid Map” button I get the message “This DNA is too big (more than 200000) or has no features”. Any suggestions?

    Also, the button for making the sequence circular seems to not work and can you set the origin of a circular sequence?

    Thanks,

    George S.

    Like

    Reply

    1. Hi George,
      The BioIllustrator is for the creation of illustrations including the plasmid map illustration from the files, so you need GenBank (.gb) or .dna, .xdna files having the DNA features. After opening of these files you can change the colors, feature name position, add restrictions site and etc. But, If you have only the sequence without features and you would like to create features for this sequence you cannot use BioIllustrator, you can use other programs like BioLabDNA or BioLabDonkey.
      Best,
      Valeriy

      Like

      Reply

  9. Hello, I have been trying to use Biodonkey and there are many inconsistencies in its function. For now, I have been trying to find ORFs, but it does not work. I select some DNA in the main window, then press the find ORF button and then I type the minimum ORF length (in this case 50bp), and nothing at all happens….I have been trying other things as well, but for now, will start with this…

    Thanks.

    NK

    Like

    Reply

    1. Hi,
      The ORF detection function was tested many times, so lets try to find the reason in your case. First, it can be that your sequence does not have ORFs with default ATG start codon. If this is the case then just select all possible start codons for both forward and reveres ORFs, set the minimal ORF length and then press the search button. Second option to figure out – you can paste the sequence, you have used, here, in the comments and I will test it.
      Best,
      Valeriy

      Like

      Reply

  10. Hi Valeriy,

    I sincerely apologize because in my previous message on October 7, 2024 at 3:17 pm I mistakenly said that I can’t make plasmid maps with the BioIllustrator app. However, the issue is actually with BioLabDNA. When I click on the “Plasmid Map” button in BioLabDNA, I receive the following message: “This DNA is too big (more than 200,000) or has no features.”

    I am not trying to include specific features like ORFs or promoters – I’m simply trying to generate a basic restriction map with some preselected enzymes using the 5.24kb SV40 DNA.

    Also, the button for making the sequence circular seems to not work and can you set the origin of a circular sequence?

    Thanks for your help.

    George S.

    Like

    Reply

    1. Hi George,
      Thank you for the info ! The plasmid Map issue with DNA without features I have fixed and the new app version (1.10) will appear, I guess, in Monday.
      About “making the sequence circular” – there is no button for this. Do you mean the origin of a circular sequence as new start ? The main window has sequence and the first letter in this text is start (1) in Plasmid map. You can change the start of the sequence in main window and accordingly the start of plasmid in the Plasmid map by putting the cursor at chosen letter of the sequence in the main window and then by pressing the button with abbreviation NS (new start) at top.
      If you are asking about the button at the bottom of right corner (with circular and linear signs), by pressing this button you change the result of restriction for circular and linear DNA sequence.
      Best,
      Valeriy

      PS. (14.10.2024)
      The new version (1.10) is in AppStore

      Like

      Reply

  11. Hi Valeriy,

    I try to open .xdna-files with the BiolabDonkey Software (I use Version 5.11 (81) on a Mac mini (M1, 2020) running Sequoia 15.3.1. I use the ‘open a file with extension…’ button, but the program crashes every time after I choose a file to open. Any ideas on how to fix this?

    Thanks,

    Mirjam

    Like

    Reply

  12. What is the difference between BioLabDonkey and BioLabDNA? There seems to be a lot of overlap between them.

    Like

    Reply

    1. Hi,
      The BioLabDonkey has the following additional functions absent in BioLabDna – PDB viewer, Differential analysis of RNA (mRNA and miRNA), GenBank protein features annotation, Bio-image analysis functions (calculation of gel/blot band intensities, counting of cells/colonies), Calculators. The automatic DNA cloning procedure in BioLabDonkey is different, there’re explicit tabs for insert, vector and product DNA. In BioLabDna, first, DNA insert should be copied in general buffer and then the insert can be pasted in the vector DNA automatically. Other functions are the same in both apps.

      Like

      Reply

  13. Hi,

    The values ​​determined in western blot analyses in the BiolabImage program are not copied. There is an option to send as PDF or e-mail, but it would be more practical to select and copy the values ​​on the analysis screen. Also, the analysis is done according to the lowest density band, but the fold increase needs to be rearranged according to the control group. It would be more useful if the control group was assigned from the selected areas. Will there be an update?

    Like

    Reply

    1. Hi,
      I have implemented what you have asked: 1) the first calculation of band intensities is done relative to the lowest density, and then user can select any row in the table as a new reference density band and press again the calculate button – the app will recalculate the ratios relative to the selected value; 2) user can select the rows in the table and copy the numbers of the selected rows by two finger click on touchpad into the general buffer to paste after. I will send the new version to AppStore today and it will be available likely in couples of days.
      Best

      Like

      Reply

  14. Hi, here are limited shapes in the BioIllustrator program. Adding shapes such as cell culture (culture flask, cell line images, incubator, etc.) and in vivo animal images (mouse, rat, cat, dog, tissue samples: liver, brain, muscle tissue, heart, etc.) can be beneficial for the program and users.

    Like

    Reply

    1. Hi,
      Thank you for the suggestions. You are right, more shapes will be beneficial, albeit some of them which are often used are present (mouse, rat, muscle tissue, incubator). If you need some particular ones, it would nice if you can post here a list of the prioritized shapes/images (to make them takes more time than coding and it will be pity if they are rarely used).

      Like

      Reply

      1. Thank you for your interest,
        For cell culture studies;
        Cell flask, image of cells cultured in culture petri dish, metastasis image, vein and arteries, chemotaxis image, angiogenesis, tumor tissue,
        For animal studies; Rat and mouse brain image, liver, lung, colon, kidney, muscle and fat tissue images, kidney tubule structure etc.

        These suggested images can be used by many researchers.

        Like

Leave a reply to Krishna Kurthkoti Cancel reply