Software Tools - Science topic

Software like IR Biotyper uses FTIR spectral analysis combined with machine learning to identify bacteria by comparing their unique infrared fingerprints to reference databases.

check out https://asreview.nl/

Hello Pratik Ramjivan Shriwas,

it is normal, that you have several genes with the same name. You should use all of them. If you find only one of several IDs with significant differences, you should be skeptical and should find the reason. Otherwise, if all or the majority of them are significant as well, then you are on a more secure side. If you have genes with really all zero values you could remove them from your data analyses or replace the value 0 with a small number 0.001 (that looks to be faster).

In other words, modernization in the education of civil engineering involves shifting institutions from traditional lecture-based teaching to interactive and problem-solving approaches, emulating on-site scenarios. Simulation tools, AR, and digital twins in understanding complex structure and material will make students understand better. Innovation will be encouraged with the multidisciplinary approach in combining civil engineering with environmental science, robotics, and geospatial technology. Equally, universities should encourage entrepreneurial thinking by calling on students to provide sustainable solutions for infrastructure and smart cities. In this way, by provoking adaptability and lifelong learning, the future civil engineers will be able to thrive in the constantly developing industry.

Gaurav H Tandon

Building on Rudy J. Richardson's insightful recommendation, Origin Pro is excellent for creating 3D plots, with the added benefit of animation options for different views. For more customizable and interactive plots, Python (with libraries like Matplotlib, Plotly, or Mayavi) and R (using ggplot2 and plotly) are great choices. Additionally, KNIME offers powerful analytics integration. Simulations Plus ADMET Predictor/Modeler is perfect for molecular descriptors, while ChemAxon and Chimera are great for molecular visualizations.

Are you designing a topology for wet etching or PCE of sacrificial layers?

Even though I have never done this kind of a simulation before, I am pretty sure that Blender + a few extensions could help in setting up such a simulation. The 3D environment (in this case: the room) can be modelled quite easily in Blender. I did some research on a variety of softwares available and the features that they offer. Radiance seems to come out on top (not a very steep learning curve and seems to check all the boxes: shadows, material properties, reflections, etc).

So yeah Blender + Radiance could be a potential solution.

Reading through the medium article, "CRAAP Meets AI" :

Dr D. Bernard explores the role of AI in academic research, discussed the importance of rigorously evaluating information when conducting research. She emphasized the use of the CRAAP Test, which stands for Currency, Relevance, Authority, Accuracy, and Purpose. A possible and effective fundamental tool for ensuring the credibility and reliability of sources for academic writing.

She noted that while AI tools like ChatGPT and Perplexity can provide rapid access to information, they also have limitations. He cautioned that AI models can sometimes provide outdated information, draw from non-credible sources, and struggle with contextual understanding.

To address these limitations, Dr. Bernard recommended applying the CRAAP Test to AI-generated information. This involves verifying the currency of the information, ensuring its relevance to the research question, checking the authority of the sources cited, confirming the accuracy of the facts presented, and understanding the purpose behind the information.

By combining traditional research methods with modern AI tools and applying the CRAAP Test, researchers can ensure the quality and reliability of their research. Dr. Bernard emphasized the importance of maintaining research integrity and vigilance in the age of AI.

Reference

Bernard D. (n.d). CRAAP Meets AI. Medium. https://medium.com/@drbernard21/craap-meets-ai-8a489389149f?sk=8d734a402e6f9ebaefee782ec7559f9f

What is your point of discussion?? I see only an instruction how to do things properly.

Use GROMACS for the same

(https://www.gromacs.org/)

For plotting graphs n analysis you can use QTgrace.

Regards

Qualitative research is always going to be subjective, so the word "validity" is seldom used. Instead, your suggestion to minimize bias is the preferred language, and working in teams is a good way to do this.

Going back to the participants with your tentative findings is known as "member checking," and the original source for this recommendation is Guba and Lincoln (1985), Naturalistic Inquiry. But do not take this a comparison between your researcher-generated interpretations and the "truth." Instead, it is up to you to reach your own conclusions, while certainly taking your participants' point of view into account.

Thank you for the insightful comparison between RMS and the Hilbert Transform in EMG analysis Dr. Safaa Ismaeel

If your project is particularly large and complex, I recommend starting with CapdetWorks or WaterCAD to manage the multi-phase estimation and then using additional tools like Civil 3D for detailed design and modeling.

Yes, it is feasible to implement user-defined material models in ANSYS and MSC.MARC using C or C++. Here’s a guide on how to proceed with this approach:

ANSYS primarily uses Fortran for user-defined material models (through usermat.f), but you can integrate C or C++ code through the following methods:

MSC.MARC typically uses Fortran for user subroutines (e.g., hypela2.f), but similar to ANSYS, you can integrate C/C++ code as follows:

By using these methods, you can leverage C or C++ for complex material modeling tasks while still using Fortran as the interface within ANSYS or MSC.MARC.

Hello Dr. Waqas I have downloaded one zip file and I have sent you through Email. Please check may be this will help you.

Some research articles:

Regards,

Joachim

As Valerio Pampanoni mentions, these could be replicated in PowerPoint - if one has beyond expert level PowerPoint skills and very experienced with the dark corners of the PowerPoint interface. I have 30+ years experience with all sorts of graphic arts software and CAD, so although I could do it, and have at times done similar art, but only with a gun held to my head.

This isn't a negative on PowerPoint, it simply wasn't intended for this complexity. It would be far easier, even without much experience, to use a tool like Adobe Illustrator or the free Open Source application Inkscape ( https://inkscape.org/ ) - and that skill would be a very useful as you move forward in your career.

The big drawbacks coming immediately to mind are that PowerPoint has no 'Layers', so you can't lock or hide what you don't want selected as you work, PowerPoint has very weak ability to make and apply styles, very limited drawing tools, and the fatal flaw, if you intend on professionally publishing is it is wretched at importing external assets and exporting in pre-press quality formats (font handling, masking like those images inside of hexagons, etc.) for instance). I use Illustrator and Inkscape pretty much interchangeably.

The best choice for you will depend on the specific type of features you're interested in extracting (e.g., land cover types, buildings, roads), your level of expertise, and the software you're already familiar with.

Automated Methods and Software Tools

a. Object-Based Image Analysis (OBIA): OBIA is a powerful approach that segments images into meaningful objects based on spectral, spatial, and contextual characteristics. These objects can then be vectorized, offering a more accurate and efficient alternative to pixel-based methods. Software options include eCognition, Trimble eCognition, and Intergraph GeoMedia.

b. Image Classification Algorithms: Supervised and unsupervised classification algorithms can help you automatically classify pixels into different categories. You can then convert these classified images into vector data. Many remote sensing software packages, such as ENVI, ERDAS Imagine, and ArcGIS, include these algorithms.

c. Specialized Tools:

i. Semi-Automatic Classification Plugin (SCP): This QGIS plugin provides tools for the semi-automatic classification of remote sensing images.

ii. Orfeo Toolbox (OTB): OTB is an open-source library for remote sensing image processing, including tools for image segmentation and vectorization.

The Workflow

1. Preprocessing: Ensure your RS images are georeferenced and radiometrically corrected.

2. Image Segmentation: Divide your images into meaningful regions (objects) based on their spectral, spatial, and contextual properties.

3. Feature Extraction: Extract relevant features from the segmented objects, such as spectral signatures, shape, texture, and context.

4. Classification/Vectorization:

a. If you're using object-based methods, classify the objects and then vectorize them.

b. If you're using pixel-based methods, classify the pixels and then convert the classified image into vector data.

Present software are more driven by Systems house and Product selling point of view. Most of them suggest corrective measures by adding some electrical component. The fundamental engineering studies and Improvement at Design basis levels are not there.

Lot of works need to be done as we need to establish the equivalence between the legacy system of Rotating machines to New Power Electronics Based systems.

Hey there Shahzor Memon!

Creating a simulation model for railway track dynamics is a fascinating challenge. Here's a step-by-step guide to get you Shahzor Memon started:

1. **Define Objectives**: First, determine the specific aspects of track dynamics you Shahzor Memon want to simulate. This could include factors like train speed, track geometry, loading conditions, etc.

2. **Gather Data**: Collect relevant data such as track geometry, material properties, train characteristics, and environmental conditions. Accurate data is crucial for a realistic simulation.

3. **Choose Simulation Software**: There are several software tools available for dynamic analysis of railway tracks. Some popular ones include SIMPACK, VI-Rail, and OpenTrack. Choose the one that best fits your requirements and expertise.

4. **Model Creation**: Start building your simulation model within the chosen software. This involves creating a digital representation of the track, including rails, sleepers, ballast, and any other relevant components. Pay attention to detail and accuracy in your model.

5. **Define Boundary Conditions**: Specify boundary conditions such as initial velocities, applied forces, and constraints. These conditions will influence the behavior of the track during simulation.

6. **Apply Loads**: Introduce loads onto the track model to simulate the effects of trains passing over it. Consider factors like train speed, weight, and acceleration.

7. **Run Simulations**: Once your model is set up, run simulations to analyze the dynamic behavior of the track under various conditions. This may involve performing multiple runs with different parameters to understand different scenarios.

8. **Interpret Results**: Analyze the simulation results to gain insights into the track's dynamic behavior. Look for factors such as track deflection, stress distribution, and fatigue life.

9. **Iterate and Refine**: Based on the results, refine your model and simulation setup as needed. Iterative refinement is key to developing an accurate representation of track dynamics.

10. **Validation**: Validate your simulation results against real-world data or existing empirical models to ensure accuracy and reliability.

Remember, simulation modeling is both an art and a science, so don't hesitate to experiment and iterate until you Shahzor Memon achieve satisfactory results. Good luck with your railway track dynamic analysis!

Dear Doctor,

Actually it is really confusing as I came to know a new website named UNDETECTABLE. AI where even generated texts by AI can't be detected. We need to agree on the huge interference of AI in today's research!!

Brijesh Kumar Singh

Designing KASP (Kompetitive Allele-Specific PCR) markers for genotyping involves several key steps. First, identify the target SNP (Single Nucleotide Polymorphism) for genotyping. Then, design allele-specific primers that specifically amplify each allele.

These primers should have a competitive element, typically a tail or a universal tag, to allow discrimination between alleles during the competitive PCR step. Validate primer specificity and efficiency using appropriate controls. Finally, optimize PCR conditions for genotyping accuracy and reproducibility.

For designing PCR primers compatible with KASP technology, several software tools are available. KASP Designer by LGC Biosearch is a widely used and reliable tool for designing KASP assays.

It helps design allele-specific primers and provides information on potential amplicon size and SNP position. Another option is Primer3, a versatile primer design tool that can be configured for KASP primer design by specifying parameters such as allele specificity and competitive tails. Both tools are accessible online and can assist in the efficient design of KASP markers for genotyping purposes.

In teaching bachelor's students digital marketing, i use the following tools: Yandex services (Wordstat) and PPC-Help for collecting the semantic core; Popsters and SimilarWeb for competitor analysis; Supa for creating creatives; Miro for collaborative work on consumer profile development.

I have downloaded it but its Run menu and New Project menus are disabled. I have downloaded a DEMO version. Any hint?

Hi,

Check this out :

MOE does it

For regression analysis, there is also this, with a new algorithm:

You can try it for 25 days. Comments welcome!

Mr. Wali Mohd Dar, thank you for this enlightening questions. I will try to answer them in my upcoming articles. I will send you an invite. Sincere regards

Professor Annemarie Honegger, I have a very important question:

I obtained a Rosetta score for my antibody-antigen complex (which is a ground truth since it is a stable structure and experimentally determined by Cryo-EM), so the total energy score equals to +628 (positive score). The thing is I calculated this score with the help of online docking server called "Rosetta Dock" or "Rosie" - https://rosie.rosettacommons.org/docking2, but I dont know how reliable it is...and is it a mistake by server, although I measured the energy quite few times?? Should I score by regular rosetta in my own local server???

I have been very fortunate to be involved with experimental watersheds, gauging streams and interacting at times with Official stream gauges, installing, measuring flow, data analysis, etc. In the US, the US Geological Survey is the preeminent agency for this work, and the US Forest Service and many Universities, and States set up their own experimental catchments, or specific needs for stream gauging, water balance, flood and drought estimates, and often rainfall and other meteorological associated data. The long term network of water based stations has been relied heavily upon. The guidance provided by USGS based on this information is extremely helpful, but as suggested by other commenters, hydrologic analysis may include other factors. My training, experience did not depend on flood models or software for the most part. It was more data based, observational and included site evaluations, such as for culverts, bridges or other crossings, evaluation of floodplain or flood prone areas for example. To the greatest extent, estimates of flooding had a strong relationship to watershed size, with considerations associated with physiographic area, topography and rainfall amount and frequency data. Presence of accumulations of large wood, signs of excess sediment or bedload, potential of landslides would be some of the considerations in assessing conditions. I would recommend if models are used, to try to validate them first with existing data available. If no data, when you drive your roads and highways, as you come by stream crossings, try to find when they were installed, have they failed or been overtopped/damaged, measure their size, use GIS or topographic maps to determine watershed size, aerial photos for land use, geology and soil maps, if you have time bankfull and floodplain cross section, any local information on past flood(s), etc. If you ever have a major flood, when travel is safe, drive the roads, looking for flood water marks, signs of culvert or bridge overtop with deposited debris, sediment, damage. Flood gauging high water can also be done with crest gauges. If culverts and bridges remain in place for many years or the structure lifetime, the local guidance is probably sufficient.

One approach is to create a funnel plot of the diagnostic test accuracy estimates for each study, which can reveal whether small studies with lower diagnostic test accuracy estimates are disproportionately missing from the literature. Funnel plot is a scatter plot of test accuracy against a measure of precision, such as standard error or 1/square root of sample size. A funnel-shaped asymmetry in the plot may suggest publication bias. The Egger's test or the trim and fill method can also be used to formally test for funnel plot asymmetry.

Another approach to testing for bias is to use statistical tests, such as the Peters test or Duval and Tweedie's trim and fill method. These tests are used to estimate the amount of missing studies and to correct for publication bias. These methods can be applied to both phantom and coffee-break studies.

It's also important to note that even after testing for bias, it is important to consider the risk of bias when interpreting the results of the meta-analysis. This may be particularly important when the studies are generally small, or have high risk of bias. Additionally, it is important to consider the external validity of the study by assessing the generalizability of the results, how well the sample represents the target population, and how well the index test being evaluated perform in the real world.

Nice

I use wordart https://wordart.com/

Variations on this question have been asked here several times. The basic conclusion is that all of the major qualitative data analysis programs (ATLAST.ti, Dedoose, MAXQDA, and NVivo) do essentially the same thing, but there are meaningful differences in how they implement these procedures.

The best thing to do is examine the training materials that these programs make available at their websites to determine which one feels most comfortable to you.

Thank you Thamoddya Rashmitha, Nnodi Joy and Keith D. Foote for the recommendation.

My pleasure, feel free to contact me, I will be in touch with you.

Thanks

Dear Md. Rifat Hossain

I suggest you use GULP. It can calculate the properties of the structure and fit the MD potential and force field with the ab initio and experimental data. It supports many types of potential and forcefield. You can even mix the different potential and force fields if one kind of potential is not enough.

You can check the example and manual of the software for technical details.

Best Regards,

For popular species you can use UCSC In-Silico PCR

Dear Anjali,

You can do it in MATLAB programming. A high-quality/resolution/dpi graph can be plotted with the help of MATLAB software by writing just a simple program.

Thanks,

COMSOL MULTIPHYSICS or FDTD are highly recomended

Hi Professor, I have heard about FlexSim (https://www.flexsim.com/flexsim/), but didn't use to develop such models so far.

Were you able to find out an opensource solution for this problem?

For any primer design and sequence manipulations I always used the software called Serial Cloner

an update further down the line, making use of the integrated AI via the boolean string you can create in colandr

Martin Lehmann https://mdpi-res.com/d_attachment/entropy/entropy-23-00018/article_deploy/entropy-23-00018-v2.pdf

At this moment there is no tool for signed graphs that is similar to newGRAPH. However, newGRAPH is upgradeable, and so by some programming effort one can add a tool that would deal with signed graphs. In addition, many commercial and non-commercial math software support work with weighted (and so, signed) graphs.

zotero

Why don't you try some Python pre-existing code?

If I'm understanding your question right, I've had some success using noun phrase extraction using Python TextBlob (https://www.pythonprogramming.in/how-to-extract-noun-phrases-using-textblob.html).

Python NLTK is another option but involves a lot more reading and trial and error. TextBlob simplifies the process and from my experience gave better results.

Either way, you'll end up with a list of terms that you'll have to manually verify, but the code should do a lot of the work.

Start with sci-kit learn. https://scikit-learn.org/stable/

Once you are good with sci-kit learn, then you move to PyTorch or TensorFlow.

You are welcome dear Omid Sadeghian

Sincerely,

Danial.

sure

Try BURAI but only for building/ optimizing the molecule, not for band(any other property) calculations.

I would suggest https://www.connectedpapers.com/ for finding the most appropriate references on a given topic. I recently discovered this and it's free.

Dear Prof. Bryar A. Hassan,

There is no need for this software. The issue is not complex. It is just to compare the authors' names with the references. For more information, please take a look at the following useful RG link:

Nibras Husein Mhawesh – that is not an answer, that is spam. Please do not reply to questions unless you have something to contribute. If you are trying to improve your RG score, you are going about it the wrong way. You are simply looking foolish. I note that you have left this "answer" on about 90 questions so far. That's enough. RG is for research.

There are many FEA software's packages that are used to simulate the dynamic response for a vehicle. I think you should use the one you are acquainted.

sourceso for Matlab!

Here is one of the best source for learning ANN:

ARCGIS AND ERDAS

I recommend QuakeMigrate: https://github.com/QuakeMigrate/QuakeMigrate

Dear Adil Sunny

The simulator SCAPS-1D is used to make many solar cell simulations which can be utilized to match the experimental work. And so, it can be used to reliably simulate the solar cells provided that they are one dimensional. It also agree with the simulation results from very powerful simulators such as the TCAD SILVCACO simulator.

I would like that you follow the papers in the links:

Best wishes

I have experience in Vosviewer and biblioshiny (R).

Hello,

You absolutely right in following the conventional method of finding out the annealing temperature. However, if you want to use available tools to get the desired annealing temperature then you can use https://www.thermofisher.com/in/en/home/brands/thermo-scientific/molecular-biology/molecular-biology-learning-center/molecular-biology-resource-library/thermo-scientific-web-tools/tm-calculator.html

Thank you Mohamed-Mourad Lafifi

I read all of the literatures you mentioned. Most of them still use GP of the built-in already developed software in Netlogo except An adaptive agent-based model of homing pigeons which was very informative and inspiring!

Thanks again!

PointVue software for visualization and lastools for rasterization

Taking pictures of samples is crucial to my research

https://biorender.com/

Please provide your email id and I will share it

Hi Mohamed,

I had the same question, and I addressed it like this:

I looked for the target gene/transcript in NCBI, found the fasta sequence. This is in most cases the CDS of the gene. Then I doublechecked whether this gene HAS an additional 5'/3' UTR in the transcript. ENSEMBL has also a bacterial platform, which is great. For my target gene, the same sequence was found without additional UTRs. So I assume it just hasn't any (Which might be true for many genes, as it's polycistronic RNA).

But, if you have found a better solution, I'm very happy if you could share it.

Dear Algis,

Packmol is a free software for building initial Configurations for Molecular Dynamics Simulations and makes it easy to create ordered systems, such as lamellar, spherical or tubular lipid layers.

I hope you found this useful.

Dear Sir,

Cloud manufacturing software gives manufacturers full control over inventory control, sales order management, quality control, and material requirements planning from anywhere and with any device connect to the Internet. These cloud-based systems won’t be installed on your own computers, so you’ll save time on implementation, updates, and IT support. Since these systems are web-based, you can also access the system from any operating system whether you have Windows or Mac, or are looking to access with a mobile iOS or Android device.

Some Cloud manufacturing software are mentioned below:

Plex Cloud ERP is a cloud manufacturing ERP software that helps lower costs while scaling seamlessly with your business. Katana MRP, MRPEasy, Acumatica ERP, Odoo, NetSuite ERP, OptiProERP, Sage 100, Rootstock Cloud ERP etc.

It is a good question

Hello,

The best software isn't free. It's expensive. You can try the PKMP trial version https://aplanalyst.com.

PSCAD/EMTDC would be suitable.

Do you have any known splice variants that you can use as a reference sequence? That would at least help put your reads into groupings by similarity.

Is it possible to do a Bayesian reanalysis, from OR data, which are converted to r-correlation values to estimate the Bayes factor?