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PCs - Science topic
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Questions related to PCs
Dear all,
I have installed GPU GROMACS 2023 on two PCs, and one is working without errors. However, the other one gives a segmentation fault (core dumped) error during the gmx run. I launched Valgrind to check memory using the following command:
$ valgrind --leak-check=full --show-leak-kinds=all gmx mdrun -deffnm nvt -v
The results are provided in the attached text file.
Please give your valuable advice on how to solve this problem.
Sincerely,
Alisher
Dear all,
I need the collaboration of native speakers of English around the Maule, Ñuble, Bio-Bio, Metropolitan or O'Higgins regions (Chile) as participants in my PhD. thesis. The participants will be asked to listen to and type recorded words uttered by Chilean EFL trainee teachers. The data collection could also be carried out online, but it would require the installation of computer software on the participants' PCs and copying some files.
Thanks in advance.
What techniques are required for identification.
How weights (WQI) derived from relative loads and eigenvalues associated with water parameters in principal components (PCs) are calculated? I need help
To diagonalize a covariance matrix 500+x500+ is extremely difficult, almost impossible. To maximize a mean squared projection of the vectors on some direction a=(a1,a2,.....a500+) You are to solve a systems of 500+ nonlinear equations. What is the rest? Heuristic methods like genetic algorithm, ant colony, simulated annealing etc ?
I wonder when people easily say: "We've considered first 2/3/4.. PCs!"
can someone provide an answer if it is possible to use IPython for parallel computing on Windows PCs, and if so how should connections be made?
It is a known fact from the literature that phytochelatins (PCs) are Cys-rich peptides responsible for cadmium detoxification. Is it indeed the real (or only one) function? What about plants/fungi/worms living in a cadmium-free environment? Why they need PCs? How does induction work in a cadmium-free environment? The fact is that organisms have it even if there is not cadmium around. Any smart suggestions? The answer is probably not trivial.
I would like to ask for some advice for building a personal computer for general home use and bioinformatics (mainly molecular dynamics, like CUDA calculations in GROMACS, AMBER, ect) Budget is somewhere around 1500$.
1) Is there any preference between Intel or AMD for bioinformatics? For example, core i5-9600kf vs ryzen 5 3600. Like probable optimization issues of software for the processor architecture? I have heard that AMD is better for linux, but i am not sure about it
2) I already have Nvidea RTX 2060 super and GTX 970 from my old PCs. Can i use them both for CUDA calculations?
3) Is there anything special that needs to be considered in motherboard choice for CUDA calculations/bioinformatics?
I am using PCA to extract major meaningful data from many different parameters that are embedded in my remote sensing satellite imagery. I know that PCA is a dimension reduction model and the final components are perpendicular to each other and the very first PCAs are the most important ones and can explain the major part of my data's variance.
Since I am using R studio to extract my PCs, I first calculated the normalized matric and then proceed with the eigenvalues and eigenvectors. my first PC has around 80 percent of the total variance and a higher association with all parameters.
The only question here is that how can we physically explain the PC1 or PC2? what are their numbers tell us? imagine we have a PC1 range from -10 to +25, so how can I define the exact meanings behind these numbers?
Hello everybody
I am eager to know what is the procedure in software like Catia, Cloud Compare, Geomagic or etc, that remove noise from Point Clouds(PCs); especially when the PCs does not contain RGB or intensity information and it just contains 3-D coordinates of points. (e.g.PCs are obtained from laser scanner. )
Thanks in advance
Hello All,
I have a very large dataset. After computing the PCA I have selected its first and second Principal Components (PC).
In the attached file the scatter plot of these two PCs is illustrated.
I want to use these two PCs to classify two tasks.
Do you think is there any way or any transformation to change the feature space for separating these two PCs?
Thanks,
Hamed

In support of crime prevention the human monitoring systems are widely deployed in companies, schools and elsewhere. There are number of effective methods to predict the migration route of a person in a crowd by using high-order particle filter and online-learning. There are method focused on group structure to improve tracking accuracy in a situation when the detection ranges of cameras overlap.
Papers:
M. Shiozuka, T. Yotsumoto, K. Takahashi, M. Nishiyama, T. Kawamura, and K. Sugahara, “Countermeasure to Human Recognition Error for Agent-based Human Tracking System,” 12th International Conference on Mobile Ubiquitos Computing, Systems, and Technologies (UBICOMM2018), pp. 65- 70.
M. Shiozuka, T. Yotsumoto, K. Takahashi, T. Kawamura, and K. Sugahara, “Implementation Example with Ultra-Small PCs for Human Tracking System Based on Mobile Agent Technologies,” 11th International Conference on Mobile Ubiquitos Computing, Systems, and Technologies (UBICOMM2017), pp. 73-78.
Y.J. Cho, S.A. Kim, J.H. Park, K. Lee, and K.J. Yoon, “Joint Person Re-identification and Camera Network Topology Inference in Multiple Camera,” arXiv:1710.00983, 2017.
Smart phones, tablets, smart PCs, smart watches and many other smart devices lead to new life style. Mobile applications is the new smart human industry. Facebook, twitter, Instagram, Uber, Careem, and many other applications did not involve hundreds or thousands of employees. Just few smart developers and some softwares and laptops to create such applications that value billions of $s.
Uber and Careem exploits the new generation of mobile phones and high connectivity to bring an efficient and costless transportation solution. In the coming years, the current classical public transportation will be completely reshaped. No more classical taxis, trains, etc. Everything will be replaced by smart and on demand cars and buses using the smart phones and location based services like GPS.
Do you think emerging and new research topics should be oriented towards these new features and technologies.?
I have a scaled PCA biplot of the first two PCs of a data set with 43 observations and 5 variables.
The biplot indicates certain relationships between variables, based on the angles between the vectors. Some variables are positively correlated, others are negatively or not correlated at all. Why then, if I calculate and plot a Pearson's correlation between two columns in my data set, would the relationship be different from what's indicated on the biplot? (i.e. Pearson indicates a strong and significant positive correlation, but biplot shows vectors with an angle less than 90 degrees?)
Note that all my variable are highly positively correlated.
I am using PCA to reduce the number of dimensions in a kinematic assessment tool (there are currently >100 metrics over 3 tasks).
My intention was to run a PCA to reduce the number of dimensions (on one dataset) into theoretically-meaningful constructs (i.e. items related to "Speed", "Accuracy" etc.).
Once these new PCs had been established, I was planning on then testing this new structure on different data using CFA. Is this appropriate? Or is there an alternative method to achieve this same outcome?
Thanks in advance
Hi, Does any one know how to stabilize phytochelatin during analysis. I know it should be kept in -20 and it's only stable for maximum 4 h in room temperature but I'm looking for something to keep PCs stable for longer hours.
I used MVD for docking, it produces different results everytime,even whn I ran it on same ligand and receptor, and the differences are more obvious when I operated it on different PCs. Why is it so? Please anyone suggest me how to obtain a reproducible result form MVD. Thank you
Hello,
I've used the procedure proposed by Marrapu et al. (2015) --> To synthesize di-C:8, di-C:12 and di-C:18 glycero-phosphocholines, I've followed the procedure 6a-K in the reference above (with 5 eq. acyl cholrides for 1 eq. GPC for all). I've obtained my di-C:18 successfully with a yield near 100%. In contrast, I got less than 5% of di-C:8 and di-C:12 glycero-phosphocholines!
Is there any researchers who faced the same problem for short chain PCs using this protocol? What could be the problem?
Thank you,
Nabil Adrar
Is there a difference in average age among computer buyers based on their preference for Mac or PCs?
Guys, I need help! I believe the DV is Age which is being measured and the IV are the choice of computers? HELP
It is hard in classes, academic as well as in customer organizations, to protect the learning experience from disruptions and distractions. This problem has grown with omnipresence of connected devices such as smartphones, tablets, and laptop PCs.
Often, one is not in a position to force students to leave these items in their bags and closed. What are great recommendations to protect the learning (and teaching!) experience?
Hello!
I am trying to run DAPC analysis in my genome-wide dataset incluiding 188736 genotypes for 188 individuals from 18 different geographic populations. I already know there is some genetic structure in the dataset, at least 2 or 3 groups could be defined. However, when running "find.clusters()" function in order to define the most plausible number of groups that could explain my dataset I obtain strange plots of "Cumulative variance explained by PCA" and "Value of BIC vs number of clusters". The cumulative variance should be higher in the first PCs and decrease as we look at the next ones, showing a curve in the graph up to the 100%. Furthermore, the BIC graph should show an elbow at some point with the smallest level of BIC and do not to represent such a perfect line.
Do you have any idea about why obtaining these results and what do they actually mean? Could it be because the amount of genotypes and samples is such high that the function cannot work with them?
Thank you in advance.
André


Given current state of pollution in the seas and oceans with plastic and other waist products and ever increasing volume of electronic-chemical devices, such as cell phones, tables, PCs, laptops, home electric appliances and plus, it is critical to develop proper methodologies and strategies to eliminate, ideally recycle all the waist all over the world. What smart technology practical solutions are or will be available to recycle and eliminate a global pollution?
Hi I want to find out if there is statistical significant separation between the enzyme group and non-enzyme groups for the CD type I proteins using Principle component Analysis. Using parallel analysis, I found out that 10 PCs should be retained. Using two sample Hotelling's t-squared test and F-statistics, I found out that the enzyme and non-enzyme group in my score plot is separated significantly( I used this paper as my reference for analysis: http://www.sciencedirect.com/science/article/pii/S0169743911001754). My question is: Does Hotelling's T-squared Test for two samples (PC1 and PC2 score values) will give the same F-statistics as using Hotelling's T-squared for 10 PCs ? I am assuming "No". But, can I say that by using first two principle components will give the similar results as using 10 components. I have problem on how to perform Hotelling's T-squared test for more than 3 variables in Excel or SPSS.
I am looking for the scoring instructions for the PCS and MCS of the SF-36. Thank you.
My advisor has a Mac and uses Text Wrangler (which converts to fasta) and Se-Al (for mass editing) neither of which works on PCs. I've been having difficulties getting other programs to work. Any suggestions? Thanks for the help!
Principal component analysis (PCA) to obtain the principal components (PCs) that best fits the shape of the face in order to relate the SNP data with that PCs by using the partial least squares regression (PLSR) method as it is explained in Claes et al. 2014?
Don't understand very well the methodology there explained.
Thanks in advance.
Hi Professors, I am conducting a research about adoption of mobile technologies in Palestinian schools from teachers' perspectives. I focused on tablet PCs as a specific type of mobile technologies because this innovation (tablet PCs) is going on in Palestinian schools. I know there are a lot of models and theories about identifying factors that influence adoption process. Some of these are UTAUT and Roger's theory (Diffusion of Innovation). Which one is the best. My data collection instrument is semi-structured interview and weekly lesson plan.
Thank you
I am having huge number of independent variables which are highly correlated and I want to run clogit. I tried all combinations of independent variables. It is a very laborious process. So I tried PCA and run the clogit with PCs scores, is it correct to use PCA before running clogit?
Hello, I am new to handle pc3 cell. I have thawed two times this cell, both times after thawing, the cell grows but as I subculture it the cell undergoes apoptosis. I am using RPMI 1640 as subculture media. Please suggest how I overcome this?
Thanks
What is the methodology to decide required number of PCs? Can I extract PCs from a single image?
I want to develop a microcontroller based system which can communicate with PC/Laptop through USB port. (As simple as possible eg. toggle leds connected to any port of microcontroller when any key is pressed from keyboard).
I worked on atmel's 8051 and atmega microcontrollers. So these families will be preferable to me.
What is the best PC program for calculation of the stability constants of the binary systems from Raman spectroscopy data?
I'm looking to undertake research in this area, any guidance is appreciated
I developed a FORTRAN based model for the heating and evaporation of multi-component (automotive fuel) droplets. When replacing the large number (100s) of components with smaller representative number of components, the CPU time will decrease significantly. For a given PC, what other factors apart from the format of the written code, routines, subroutines, syntax ..etc., can increase the CPU efficiency of the model?