Where can I find a complete list of oncogenes and TS for NCI-60 cell lines?

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How to extract "Angle distribution" and number of "SP hybridization" in a trajectory output file (pdb/xsd)?

Hello everyone I did my molecular dynamic simulation by Materials Studio. I cannot extract some properties from my output including "Angle distribution" "pore size distribution" the number of "SP...

28 May 2021 4,221 0 View

How to execute dump.dcd file by VMD?

Hello, After my simulation, I created psf file and I used : vmd dump.dcd myfile.psf in TK console. But it doesn't work, and it hangs. What is the problem and is there another way to execute the...

23 April 2021 8,364 3 View

How I must write "pair_coeff" arguments for lcbop or tersoff in LAMMPS?

Hello everyone My system only contains carbon, so I used the lcbop potential: pair_style lcbop pair_coeff * * C.lcbop C But due to a problem with the pair_coeff argument, the program does not...

05 March 2021 8,488 3 View

How can pressure commands be applied randomly in Lamps?

Hello everyone. I wrote a program in Lammps that applies pressure on three axes separately. Since in reality the pressure is applied randomly on each of the three axes; How do I write the program...

29 December 2020 7,380 1 View

Repeated N-fold cross validation?

Hi! I am a bit confused with the term of "repeated" in repeated CV. In a typical cross validation problem, let's say 5-fold, the overall process will be repeated 5 times: at each time one subset...

25 November 2016 3,140 5 View

When to use FDR?

I have a problem with the concept of false discovery rate. Assuming I have a panel of 50 anticancer drugs for which their IC50 values are reported for 30 cell lines. On the other hand, I have a...

02 June 2016 8,788 2 View

Why in BiGG models, each metabolite corresponds to more than one KEGG metabolite?

Metabolites in SBML models in BiGG database contain annotations for providing additional information on other identifiers such as KEGG cpds. However, in some cases for each metabolite there exists...

21 October 2015 3,962 0 View

What is a suitable panel for normal/cancerous liver cell lines?

Hi, I plan to do some gene silencing in HepG2 cell line. However, to draw a profound comparison between normal and cancerous liver (in this case, hepatocellular carcinoma) phenotypes, a normal...

19 September 2015 2,118 5 View

Which parameters affect the choice of a tumor cell line?

There are various cell lines in literature from different cell collections (ATCC, DSMZ, etc.) or personal donations extracted from patients or just a gift from a generous researcher. However, not...

11 September 2015 6,984 6 View

How to extract gene expression and proteomics data from Human Protein Atlas?

I am trying to extract some cell-specific transcriptomic/proteomic data for cancerous tissues from Human Protein Atlas, however, it did not work out. I appreciate any cues in doing so, and if...

14 August 2015 5,400 4 View

Why Do TDS and EC Increase with Larger Wastewater Volumes, While BOD and COD Decrease?

I have carried out MFC experiments on three different volumes, 50, 500 and 1000 mL of wastewater. Results after MFC treatment shows that TDS and EC are more in larger volumes of water i.e. TDS and...

09 August 2024 9,621 0 View

Could it be a cell culture contamination?

Hello everyone! I observed in my culture (htert-RPE1 cells) an orange- red particle at the bottom of the dish. It is visible to the naked eye as a very very small red dot. Could it be a...

09 August 2024 2,824 3 View

Is there any way to quantify bacterial and fungal cells in their mixed culture?

I am working in fungal fermentation of soybean meal and there is bacterial growth in them at times. I am trying to quantify fungal cell counts and bacterial cells; but I haven't been able to do at...

07 August 2024 7,535 4 View

How to normalize and take the significance of the MTT OD values with 3 replicates for the same cell-line?

Hi, I have a question about normalizing the MTT OD values for doing the statistical analysis. So, if we have 3 different plates and we call them 3 different replicates, so, first we would...

07 August 2024 8,106 4 View

Why activated CAR-Jurkat cell could not kill targets?

Previously when I co-coluture anti-CD19(FMC63) CAR-Jurkat with Raji with E:T=5:1, Jurkat can eliminate Raji in 24h. However, when I test another CAR construct, although I can dectect totally CD69...

06 August 2024 641 2 View

Weak DAPI staining after immunohistochemistry - how to improve?

After immunohistochemistry of previously fixed in PFA and EtOH and then frozen 20 μm sections of zebrafish brain, DAPI staining is very weak (right) compared to the same sections stained without...

05 August 2024 9,637 2 View

The Curse of Evolution and Complexity?

Brain and body mass together are positively correlated with lifespan (Hofman 1993). The duration of neural development is one of the best predictors of brain size, and conception is the best...

05 August 2024 6,247 3 View

How to isolate lymphocytes from mouse spleen?

I have tried several times to isolate lymphocytes from mouse spleen, but all attempts have been unsuccessful. I tried most available protocols. I used different dissociation media (HBSS with Ca...

04 August 2024 9,913 7 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

Does long-term culture of murine Monocytes result in macrophage differentiation?

Hi, I am isolating monocytes from the bone marrow using the Mouse Monocyte EasySep kit. I want to treat these cells and monitor expression of specific markers over the course of 10 days. I will...

04 August 2024 7,282 2 View