# BioInformatics **URL:** https://forum.knime.com/c/special-interest-groups/bioinformatics/37.md [Latest](https://forum.knime.com/latest.md) · [Categories](https://forum.knime.com/categories.md) · [Tags](https://forum.knime.com/tags.md) --- ## [Chemical clustering with similarity to chemical structure](https://forum.knime.com/t/chemical-clustering-with-similarity-to-chemical-structure/82440)
**Author:** [@reinyah94](https://forum.knime.com/u/reinyah94)\ **Replies:** 1\ **Last updated:** [September 9, 2024, 3:41pm UTC](https://forum.knime.com/t/chemical-clustering-with-similarity-to-chemical-structure/82440 "2024-09-09T15:41:40Z")
Hi all, I am knew to using Knime and I am trying to do a selection of pesticides based on chemical structure. I have a data set of less than a 1000 compounds and would like to make clusters to selected 2-3 from each for… --- ## [Targeted Lipidomics](https://forum.knime.com/t/targeted-lipidomics/72981)
**Author:** [@Simon\_Kienle](https://forum.knime.com/u/Simon_Kienle)\ **Replies:** 1\ **Last updated:** [October 5, 2023, 2:56pm UTC](https://forum.knime.com/t/targeted-lipidomics/72981 "2023-10-05T14:56:58Z")
Hello Everyone, I am new in the Lipidomics field and have a basic understanding of KNIME. I now want to use KNIME and openMS to analyze my targeted Lipidomics LC-MS/MS (Agilent QqQ) data. However, I already have difficu… --- ## [How to extract data from postgresql to knime?](https://forum.knime.com/t/how-to-extract-data-from-postgresql-to-knime/65560)
**Author:** [@Valunce](https://forum.knime.com/u/Valunce)\ **Replies:** 5\ **Last updated:** [April 17, 2023, 4:37am UTC](https://forum.knime.com/t/how-to-extract-data-from-postgresql-to-knime/65560 "2023-04-17T04:37:33Z")
I want to move data of chembl\_32 into knime to analyze, therefore i take the steps as below. Currently, I take my action on the step 4 and don’t know how to process. I am very grateful if someone can guide me directly or… --- ## [How to open/read sdf](https://forum.knime.com/t/how-to-open-read-sdf/40584)
**Author:** [@Razanknime\_123](https://forum.knime.com/u/Razanknime_123)\ **Replies:** 4\ **Last updated:** [March 11, 2022, 11:45pm UTC](https://forum.knime.com/t/how-to-open-read-sdf/40584 "2022-03-11T23:45:57Z")
Hello Any idea how I can open and read the sdf after using the csv reader-openbabel-sdf writer workflow in knime? Thank you in advance --- ## [Pattern Count - Bioinformatics](https://forum.knime.com/t/pattern-count-bioinformatics/36572)
**Author:** [@Mutaz](https://forum.knime.com/u/Mutaz)\ **Replies:** 4\ **Last updated:** [October 11, 2021, 11:49am UTC](https://forum.knime.com/t/pattern-count-bioinformatics/36572 "2021-10-11T11:49:54Z")
Greetings; I am learning Bioinformatics and I am going to use Knime for solving Computational problems as I want to focus on the concepts instead of programming and I am familiar with Knime, do you think it is a good id… --- ## [Use KNIME to run remote jobs](https://forum.knime.com/t/use-knime-to-run-remote-jobs/11836)
**Author:** [@gugy](https://forum.knime.com/u/gugy)\ **Replies:** 5\ **Last updated:** [July 2, 2021, 8:07am UTC](https://forum.knime.com/t/use-knime-to-run-remote-jobs/11836 "2021-07-02T08:07:35Z")
I am a complete newbie to KNIME, but would like to use it for a very specific task: I want to use a KNIME workflow to submit Molecular Dynamics simulations to a supercomputer. The simulations will be run with GROMACS, a… --- ## [Sentence based opinion mining](https://forum.knime.com/t/sentence-based-opinion-mining/26115)
**Author:** [@Engr\_Adnan11](https://forum.knime.com/u/Engr_Adnan11)\ **Replies:** 1\ **Last updated:** [August 17, 2020, 11:29am UTC](https://forum.knime.com/t/sentence-based-opinion-mining/26115 "2020-08-17T11:29:56Z")
Basically what I want is to opinion mining on sentence based I will garb the information of vaccine related to an illness through documents grabbing node and then parse it and then want to do sentence based opinion mini… --- ## [EMBL Conference: In situ Structural Biology - From Cryo-EM to Integrative Modelling](https://forum.knime.com/t/embl-conference-in-situ-structural-biology-from-cryo-em-to-integrative-modelling/18567)
**Author:** [@EMBL\_Events](https://forum.knime.com/u/EMBL_Events)\ **Replies:** 0\ **Last updated:** [October 1, 2019, 10:48pm UTC](https://forum.knime.com/t/embl-conference-in-situ-structural-biology-from-cryo-em-to-integrative-modelling/18567 "2019-10-01T22:48:09Z")
There is an increasing awareness that mechanistic structural information on molecular machines is ideally generated within the context of intact cells in order to fully grasp how they function in a complex native environ… --- ## [EMBO | EMBL Symposium: Biological Oscillators: Design, Mechanism, Function](https://forum.knime.com/t/embo-embl-symposium-biological-oscillators-design-mechanism-function/18565)
**Author:** [@EMBL\_Events](https://forum.knime.com/u/EMBL_Events)\ **Replies:** 0\ **Last updated:** [October 1, 2019, 10:35pm UTC](https://forum.knime.com/t/embo-embl-symposium-biological-oscillators-design-mechanism-function/18565 "2019-10-01T22:35:08Z")
Oscillations are abundant - from hormonal oscillations with periods of days and months, to genetic fluctuations in the range of hours (circadian clock, embryonic oscillators), and metabolic and biochemical oscillations i… --- ## [EMBO | EMBL Symposium: Organoids: Modelling Organ Development and Disease in 3D Culture](https://forum.knime.com/t/embo-embl-symposium-organoids-modelling-organ-development-and-disease-in-3d-culture/18564)
**Author:** [@EMBL\_Events](https://forum.knime.com/u/EMBL_Events)\ **Replies:** 0\ **Last updated:** [October 1, 2019, 10:32pm UTC](https://forum.knime.com/t/embo-embl-symposium-organoids-modelling-organ-development-and-disease-in-3d-culture/18564 "2019-10-01T22:32:42Z")
The ability to grow human tissues from stem cells in 3D culture has the potential to revolutionise the drug discovery process and regenerative medicine. Building on a long tradition of cell and developmental biology know… --- ## [EMBO | EMBL Symposium: The Neurovascular Interface](https://forum.knime.com/t/embo-embl-symposium-the-neurovascular-interface/18563)
**Author:** [@EMBL\_Events](https://forum.knime.com/u/EMBL_Events)\ **Replies:** 0\ **Last updated:** [October 1, 2019, 10:29pm UTC](https://forum.knime.com/t/embo-embl-symposium-the-neurovascular-interface/18563 "2019-10-01T22:29:12Z")
Neurovascular biology is a young, emerging field that aims to unravel the molecular communication between the nervous system and the vasculature. Both the nervous system and the vascular system share striking conceptual … --- ## [EMBO | EMBL Symposium: Defining and Defeating Metastasis](https://forum.knime.com/t/embo-embl-symposium-defining-and-defeating-metastasis/18485)
**Author:** [@EMBL\_Events](https://forum.knime.com/u/EMBL_Events)\ **Replies:** 0\ **Last updated:** [September 27, 2019, 4:01pm UTC](https://forum.knime.com/t/embo-embl-symposium-defining-and-defeating-metastasis/18485 "2019-09-27T16:01:43Z")
This symposium will cover emerging key concepts of latent metastasis and dissemination of tumour cells including evolution and genetic diversity of metastasis, circulating tumor cells, stemness, dormancy and stromal repr… --- ## [EMBO | EMBL Symposium: Microtubules: From Atoms to Complex Systems](https://forum.knime.com/t/embo-embl-symposium-microtubules-from-atoms-to-complex-systems/18484)
**Author:** [@EMBL\_Events](https://forum.knime.com/u/EMBL_Events)\ **Replies:** 0\ **Last updated:** [September 27, 2019, 3:58pm UTC](https://forum.knime.com/t/embo-embl-symposium-microtubules-from-atoms-to-complex-systems/18484 "2019-09-27T15:58:35Z")
The microtubule cytoskeleton is essential for a wide variety of cellular functions, such as chromosome segregation, directed vesicle and organelle transport, cell motility and cell polarity. Impaired microtubule function… --- ## [EMBO Workshop: Microglia 2020](https://forum.knime.com/t/embo-workshop-microglia-2020/18482)
**Author:** [@EMBL\_Events](https://forum.knime.com/u/EMBL_Events)\ **Replies:** 0\ **Last updated:** [September 27, 2019, 3:54pm UTC](https://forum.knime.com/t/embo-workshop-microglia-2020/18482 "2019-09-27T15:54:31Z")
Microglia are a resident macrophage of the central nervous system at the intersection of immunology and neuroscience. They have gained increasingly more attention over the past decade as more research shows that they are… --- ## [Knime and CDD Vault](https://forum.knime.com/t/knime-and-cdd-vault/11221)
**Author:** [@hungerfordwm](https://forum.knime.com/u/hungerfordwm)\ **Replies:** 6\ **Last updated:** [November 20, 2018, 2:24pm UTC](https://forum.knime.com/t/knime-and-cdd-vault/11221 "2018-11-20T14:24:58Z")
Does anyone use Knime as a workflow for Plate-based and Well-based HTS Analytics by exporting raw data from CDD Vault (Collaborative Drug Discovery), processing the calculations in Knime, and then exporting the finished … --- ## [Reading in a protein FASTA file in KNIME](https://forum.knime.com/t/reading-in-a-protein-fasta-file-in-knime/12525)
**Author:** [@lparsons42](https://forum.knime.com/u/lparsons42)\ **Replies:** 1\ **Last updated:** [November 7, 2018, 8:00pm UTC](https://forum.knime.com/t/reading-in-a-protein-fasta-file-in-knime/12525 "2018-11-07T20:00:39Z")
I know this should be an easy task, but with a large FASTA file (say a Uniprot db with ~42,000 sequences over ~460,000 lines) it turns out to be anything but. I know we have ‘Bio Sequence Reader’ from “NGS Tools” and ‘F… --- ## [EMBL Conference: From Images to Knowledge with ImageJ & Friends](https://forum.knime.com/t/embl-conference-from-images-to-knowledge-with-imagej-friends/12203)
**Author:** [@EMBL\_Events](https://forum.knime.com/u/EMBL_Events)\ **Replies:** 0\ **Last updated:** [October 1, 2018, 3:32pm UTC](https://forum.knime.com/t/embl-conference-from-images-to-knowledge-with-imagej-friends/12203 "2018-10-01T15:32:49Z")
The conference is designed to promote interactive discussions between users and developers of bioimage analysis methods and software. The speaker line-up features researchers at the front-lines of algorithm development a… --- ## [Are there any ready2use NGS WGS workflows available for KNIME?](https://forum.knime.com/t/are-there-any-ready2use-ngs-wgs-workflows-available-for-knime/4889)
**Author:** [@mat29](https://forum.knime.com/u/mat29)\ **Replies:** 0\ **Last updated:** [August 18, 2016, 2:33pm UTC](https://forum.knime.com/t/are-there-any-ready2use-ngs-wgs-workflows-available-for-knime/4889 "2016-08-18T14:33:24Z")
Are there any ready2use NGS WGS workflows available for KNIME? --- ## [Are there any tutorials on NGS KNIME nodes?](https://forum.knime.com/t/are-there-any-tutorials-on-ngs-knime-nodes/4882)
**Author:** [@mat29](https://forum.knime.com/u/mat29)\ **Replies:** 0\ **Last updated:** [August 18, 2016, 2:31pm UTC](https://forum.knime.com/t/are-there-any-tutorials-on-ngs-knime-nodes/4882 "2016-08-18T14:31:40Z")
Are there any tutorials on NGS KNIME nodes? Need to input FASTQ data from a FASTQreader node to the NGS nodes and they don\`t accept it. Thx. --- ## [Bash node](https://forum.knime.com/t/bash-node/8502)
**Author:** [@huei820504](https://forum.knime.com/u/huei820504)\ **Replies:** 1\ **Last updated:** [October 29, 2015, 1:11pm UTC](https://forum.knime.com/t/bash-node/8502 "2015-10-29T13:11:35Z")
Dear all: I tried this node under mac and windows Even if the description of this node is that Under Windows XP (possibly others as well) use of the program cmd.exe is recommended. E.g. to run the dir command, one wo… --- ## [GroupByLoopStart](https://forum.knime.com/t/groupbyloopstart/1764)
**Author:** [@frederico.nardi](https://forum.knime.com/u/frederico.nardi)\ **Replies:** 5\ **Last updated:** [March 15, 2012, 7:04pm UTC](https://forum.knime.com/t/groupbyloopstart/1764 "2012-03-15T19:04:49Z")
Hi Thanks a lot for the very useful \[GroupByLoopStart\] node . To my eyes, this node could be included in the standard knime distribution. It is working fine for me in most of the time. But sometime I encounter…