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Hello everyone,
I’m looking for a motivated collaborator to join an ongoing research paper focusing on applying Retrieval-Augmented Generation (RAG) pipelines to a novel real-world use case. The project explores advanced ML techniques for information retrieval and pattern detection with significant practical impact.
I’m seeking someone with:
- Experience in NLP, RAG pipelines, and anomaly detection
- Strong experimental and model development skills
- Familiarity with academic writing and publications
As for my background: I’m a Master’s student in Information Technology at Worcester Polytechnic Institute (WPI), specializing in data science and machine learning. My work includes SBERT-based innovation analysis, a Streamlit-deployed recommender system, and a RAG pipeline for legal document analysis. I also have published a research paper in IoT, available on my ResearchGate profile.
Currently, I am also interning for a marketing agency in Chicago where I am working on building sentiment analysis models to help drive their social media strategy.
I’m currently collaborating with a researcher who brings 2 years of work experience as a software engineer at a top tech startup in Europe, adding strong engineering expertise to our team.
This collaboration offers shared authorship on a high-impact paper and the chance to work on cutting-edge ML applications alongside passionate researchers.
If you’re interested, I’d love to connect and discuss further.
Best regards,
Harsh Deshpande
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Are you still looking for collaboration?
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I want to search for articles about fluid-structure interaction in pipe leakage problems.
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Recent experimental studies have explored the fluid-structure interaction (FSI) in pipeline leakage and road collapse scenarios. Here are some notable examples:
  1. Experimental Study on City Road Collapse under Vibrating Load: This research utilized eight groups of indoor scale model experiments to investigate road collapse caused by pipeline seepage. The study provides insights into the dynamic effects of fluid-structure interaction on road stability.
  2. Experimental Investigation of Transients-Induced Fluid-Structure Interaction in Viscoelastic Pipelines: This study examines the behavior of viscoelastic pipelines fixed by regular anchored brackets during transient conditions. The research aims to understand the impact of fluid-structure interaction on pipeline integrity under varying operational conditions.
  3. Experimental Study Exploring the Interaction of Structural and Fluid Dynamics in Pressurized Pipelines: This innovative experimental investigation focuses on the response of longitudinal slits in pressurized pipelines, providing valuable data on the interaction between structural elements and fluid dynamics.
  4. Experimental Study of Fluid-Structure Interaction in Collapsible Tubes: This work establishes an experimental setup to study collapsible tube deformation and fluid-structure interaction within thin-walled collapsible tubes, offering insights into the behavior of pipelines under certain conditions.
These studies contribute to a deeper understanding of the complex interactions between fluids and structural components in pipeline systems, aiding in the development of more resilient infrastructure.
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An existing pipeline, designed under ASME B31.4 is planned to be converted to transport multiphase commodities, natural gas and crude oil at the same time. Besides reviewing what's applicable on the gas side, ASME B31.8 standards, is there any special conditions that should be considered for this analysis?
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Converting an existing pipeline designed under ASME B31.4 to transport multiphase commodities, such as natural gas and crude oil, involves several critical considerations. Here's a list of key factors to address:
1. Review Applicable Codes and Standards
  • While ASME B31.4 focuses on liquid pipelines, and ASME B31.8 addresses gas pipelines, neither explicitly covers multiphase flow. Ensure both standards are reviewed in detail to identify overlaps or gaps.
  • Consider whether API RP 14E, DNVGL-ST-F101, or other standards dealing with multiphase flow in pipelines may provide additional guidance.
2. Multiphase Flow Dynamics
  • Multiphase flow introduces unique challenges, such as slugging, erosion, and uneven pressure distributions.
  • Conduct a flow assurance study to understand the behavior of the gas and liquid phases under operating conditions.
  • Account for the risk of hydrate formation, wax deposition, and corrosion due to the coexistence of gas, oil, and water.
3. Pipeline Design and Integrity
  • Operating Pressure and Temperature: Verify the existing pipeline’s capacity to handle the pressure and temperature conditions of the multiphase flow.
  • Internal Corrosion: The presence of water and the multiphase nature increase the risk of corrosion. Implement a corrosion management plan, including material selection, inhibitors, and monitoring systems.
  • Erosion Risks: High velocities in multiphase flow can cause erosion of internal surfaces. Evaluate the erosional velocity limits (e.g., using the API RP 14E erosional velocity equation).
4. Flow Stability
  • Analyze the potential for slug flow, which can cause significant fluctuations in pressure and flow rate, leading to mechanical stresses and operational challenges.
  • Consider using slug catchers or separators if slugging is predicted to be significant.
5. Pipeline Modifications
  • Assess whether additional facilities are required, such as:Slug catchers to manage flow instabilities. Pressure regulation equipment to maintain safe operating conditions. Pigging facilities for cleaning and flow assurance.
  • Evaluate if the pipeline wall thickness, fittings, and supports are adequate for the new operating conditions.
6. Hydraulic and Mechanical Analysis
  • Perform a detailed hydraulic analysis of the multiphase flow.
  • Evaluate the mechanical integrity of the pipeline, considering fatigue and vibration due to fluctuating loads from multiphase flow.
7. Pipeline Materials
  • Confirm that the materials are suitable for the new service, especially concerning chemical compatibility with transported commodities and corrosion resistance.
  • Address potential issues related to sulfide stress cracking (SSC) or hydrogen-induced cracking (HIC) if sour gas or corrosive components are present.
8. Safety and Risk Management
  • Conduct a risk assessment (e.g., HAZOP or FMECA) for the new operation to identify hazards associated with multiphase transport.
  • Update emergency response plans to reflect the new operating conditions and risks.
9. Regulatory Compliance
  • Ensure the conversion complies with local, regional, and international regulations beyond ASME standards.
  • Document the pipeline's fitness-for-service through detailed assessments in accordance with applicable standards, such as API 579/ASME FFS-1.
10. Operational Considerations
  • Monitoring Systems: Install real-time monitoring for pressure, temperature, and flow rates to detect issues promptly.
  • Training: Train personnel in the operational differences and challenges posed by multiphase pipelines.
  • Maintenance: Update maintenance schedules to reflect the increased complexity of multiphase transport.
Summary
Converting a pipeline to multiphase service involves a holistic assessment of flow dynamics, mechanical integrity, material compatibility, and operational risks. A detailed engineering analysis and possibly modifications to the pipeline and auxiliary systems will be necessary to ensure safety, reliability, and compliance. Engaging experts in flow assurance, corrosion, and pipeline design is recommended for this complex transition.
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Check at our new paper on 'MLOps: Automatic, Zero-Touch and Reusable Machine Learning Training and Serving Pipelines' that won the Best paper award at the 2023 IEEE International Conference on Internet of Things and Intelligence Systems (IoTaIS 2023) held in Bali, Indonesia.
ResearchGate Paper Draft Link:
This work demonstrates how an AI/ML model can be taken to production very easily using components from the Acumos AI project and do much more by creating zero-touch ML model infrastructures using Acumos and Nifi.
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In our process, instead of using any heat exchanger, we are planning to cool the process stream using ambient air by 150 deg C. It would be very helpful if someone can suggest guideline for the same. The main concentration is on how to calculate the temperature drop if the process pipe is left bare open in the atmosphere without any insulation.
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Piyush Jain To find the temperature drop along a process pipeline, you can:
  1. Measure the temperature at multiple points along the pipeline.
  2. Calculate the temperature difference between the inlet and outlet points.
  3. Divide the temperature difference by the length of the pipeline to determine the average temperature drop per unit length.
  4. Consider factors like pipe insulation, fluid flow rate, and ambient temperature, which can affect the temperature drop.
  5. Use a heat transfer equation to model the temperature distribution along the pipeline.
  6. Employ specialized software or simulation tools to analyze the temperature profile.
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Hello everyone, I am conducting a simulation task using CEL method in Abaqus related to offshore pipeline. I would like to know how to assign different soil materials for several soil layers of Eulerian part in Abaqus, please help. Thank you so much
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Applying different materials to separate layers of an Eulerian part in Abaqus requires defining the regions within the part and assigning material properties to these regions. The Eulerian mesh in Abaqus is typically used for problems involving fluid flow, multiphase interactions, or highly nonlinear deformations, and it consists of a fixed grid where the material can move.
To apply different materials to several layers in an Eulerian part, follow these steps:
1. Define the Eulerian Domain and Partitioning:
  • Create an Eulerian part and mesh it as required.
  • Use Partition to divide the Eulerian part into different regions (layers). This partitioning can be done based on geometric features or by creating datum planes to specify the boundaries of the layers.
2. Create the Materials:
  • Define the required materials in the Materials module.
  • For each material, specify the necessary properties, such as density, elasticity, plasticity, and any other relevant parameters.
3. Assign Sections:
  • Create Sections for each material. Go to SectionCreate, select the Eulerian material type, and assign the corresponding material to the section.
4. Assign Sections to the Regions:
  • Go to the Property module and assign the previously created sections to the partitioned regions of the Eulerian part.
  • Click Assign Section → Select the regions/layers you want to assign the section to → Choose the appropriate section (material) → Click Done.
5. Define the Initial Conditions for the Eulerian Domain:
  • Specify the initial volume fractions for each Eulerian material in the regions.
  • Go to ModelFieldInitial ConditionsCreate → Choose the Eulerian Volume Fraction.
  • Assign the initial volume fraction of each material to the corresponding partitioned regions of the Eulerian domain.
6. Set up the Analysis:
  • Set up your analysis as usual, defining the step, boundary conditions, interactions, and loads as needed.
  • Ensure the mesh and the defined regions are compatible with the material behavior you expect during the simulation.
7. Verify and Run the Simulation:
  • Verify the material assignments in the Visualization module before running the simulation.
  • Ensure that the volume fractions and material definitions align with the partitioned regions to avoid errors during the simulation.
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Hi everyone, I hope you all are fine, I have acoustic data from five different sensors for an underground pipeline. I want to compute the velocity. Can someone give me some suggestions and solutions on how to compute the velocity for all these five sensor data?
Looking forward to your responses!
Thank you all!
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Wieslaw Bicz the pipe is completely empty there is no fluid so the wave is traveling through the wall of the pipe. The sensors are present on the surface while the pipe is underground at some distance. these are continuous waves. the schematic diagram is such that; one corner of the underground pipe is exposed to the surface and the tuning fork is mounted at this corner of the underground pipe. the waves are generated through this tuning corner, which then travel through the underground pipe, and sensors are placed on the surface to record the acoustic signal.
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In terms of CFD, we often analyze the stability of the error using Von-Neumann analysis, especially for FDM based problems. Should we follow the same approach for a compressible fluid flow using FVM ?
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I would do a mesh refinement study (or change the element orders). If the oscillations are resolved and converge to a specific pattern, I would conclude they are not numerical errors. However, if they change randomly in each study, I would attribute them to numerical error.
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Pigging is basically a cleansing process followed in all pipeline industries after the product has been delivered. There are many types of pigs that are inserted inside the pipeline for this process. After the cleansing has been done the product stains will remain in that pig. So, i basically need to check the residues that are there in the pig after the operation. Has anybody done this analysis in their industry, kindly share the parameters required for it.
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It seems like you're looking for information on a specific type of analysis related to the oil and gas pipeline industry, specifically regarding pig residual analysis. Pigs (Pipeline Inspection Gauges) are used in pipelines to inspect and clean them, and residual analysis involves examining what is left behind after a pig has passed through a pipeline.
While pigging operations and residual analysis are more commonly associated with pipelines in the oil and gas industry, it's less common to find specific reports or studies directly related to pig residual analysis in this context. Typically, such analyses might focus on:
  1. Residual Material Identification: Determining what materials are left behind by the pigging operation. This could include scale, debris, corrosion products, or even accumulated oil or gas residues.
  2. Quantification of Residuals: Measuring the amount or extent of residual materials left in the pipeline after pigging. This could involve volume calculations, weight estimations, or thickness measurements.
  3. Condition Assessment: Assessing the condition of the pipeline post-pigging, including evaluating any damage or wear caused by the pigging operation itself or by the residual materials left behind.
  4. Corrosion and Integrity Assessment: Examining whether residual materials contribute to corrosion or affect pipeline integrity, which is crucial in the oil and gas industry.
If you're looking for specific reports or studies on pig residual analysis, you may want to explore academic journals, conference proceedings, or technical reports from industry organizations such as:
  • American Petroleum Institute (API)
  • Pipeline Research Council International (PRCI)
  • American Society of Mechanical Engineers (ASME)
  • National Association of Corrosion Engineers (NACE)
These organizations often publish technical papers and reports on pipeline integrity management, pigging operations, and corrosion control, which may include sections or studies related to residual analysis.
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Hi,
I am developing Deep learning model(s) for a binary classification problem. The DL works with a reasonable accuracy. Is there a reliable way to extract features from DL models built with 'Keras' pipeline? It seems that the feature contribution are distributed among several layers.
Thank You,
Partho
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In Keras, leveraging the Functional API offers a reliable approach for feature extraction from deep learning models. This method involves defining a new model that takes the input of the original model and outputs the activations of the desired layer(s) using the Model class. By specifying the input and output layers accordingly, you can effectively create a feature extractor tailored to your requirements. This approach provides flexibility in selecting the layer(s) from which to extract features, allowing you to capture information at various levels of abstraction within the model. Whether it's accessing intermediate convolutional layers for image features or dense layers for high-level representations, the Functional API empowers you to seamlessly integrate feature extraction into your deep learning workflows in Keras.
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Thank you in advance to all the specialists in the field of environmental engineering in oil fields - the bioprocessing of petroleum oil hydrocarbons. I would like to share our experience in waste management of produced water and oil sludge. We will undertake a project to construct an evaporation pond for waste crude oil and polluted produced water, entitled: Reclamation of waste crude oil and soil treatment of the resulting water evaporation pit site.
The multi- project's objectives are to remediate hydrocarbon-contaminated soils for all pits, reclaim productive water pits in operation, including dry pits used in the past, close all productive water pits, and manage waste in accordance with Environmental Protection Agency (EPA) approved methods and international standards. The project's scope also includes the construction of two new evaporation pond facilities and new concrete water pipelines connecting all GOSPs to new evaporation ponds to transfer the produced water to new ponds.
I desire and ask to know about implementing unique projects that include the construction of new evaporation ponds and cement pipelines to connect them to the evaporation ponds, water produced in accordance with environmental engineering standards. If you have previous projects, I hope you share the experience of the implemented cases or any other web sources i.e. engineering standards or design of new evaporation ponds, case studies with associated waste reports. Knowing that the project site is in the onshore oil fields (desert). Please, if anyone has information that they would like to share or send, I would be grateful for your efforts and participation. This project will include studies and publications in distinguished and esteemed scientific journals.
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Believing the importance of the project where humbly worked in TPH analyais in water EPA 418.1 via FTIR Spectroscopy. Best wishes
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I am a PhD student working with human plasma looking to do miRNA-seq analysis (differential gene expression, isomer analysis and isolating the best housekeeping genes within a cohort).
I'm keen to do the analysis myself, but after doing a lot of literature searches (and YouTube tutorials) I am really struggling to do so.
Does anyone know of a useful contact, course or information pack that will help me successfully complete the pipelines? Thanks in advance!
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Hi Oenone Rodgers,
I have previously completed over 10 projects on miRNA analysis. If you require any assistance with analysis, I can provide support until your publication. I am available to work as a freelance support (my email is manishkumarsinha002@gmail.com). Alternatively, you can reach out to us at info@biostica.in.
Good luck with your project. We can connect with you for better clarity and assistance.
Regards,
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How to create a mean model per genotype from μCT scans (dicom or tiff input format) coming from different animals so we can later compare the two different population mean models.
Currently the pipeline that we use is as following:
We use a morphometric technique based on landmarks, take the DICOM file and create the 3D model using 3D Slicer. Then we place the landmarks in idav landmarks software with the aim to obtain the 3D coordinates and build the matrix and perform the form/shape analysis.
We are also able to compare the surface of two 3D models using 3D Slicer IGT extension, however we will like to be able to compare not only two animals but several more. Does anybody can recommend a way to go or any other extension or freely available software that we can use?
Or any file that we can modifiy in the command line to manually calculate the mean or surface or volumes to get the mean of the population?
Thanks in advance looking forward to reading all your suggestions!
Kind regards,
Mar
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We have software that can do this volumetrically with the μCT, CT, CBCT, MR, or any volumetric scan. Take a look at this link which describes the basic process which uses landmark points placed within each volume. The volumes are then merged to form the population average:
This works better than doing it with only the surfaces. Give it a try and let me know if you have any questions.
I wrote the IDAV Landmark software when I was a postdoc at UC Davis. Here's some information here about the transition:
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Dear All,
In my lab, we have performed whole-exome sequencing of 10 patients to see if we found any germline variations associated with prostate cancer.
I am new to projects that use sequencing and am a little lost on how to analyze these results.
Can anyone suggest to me an app, approach, or pipeline to analyze these results?
I have my data in fastq files and understand a little bit of R.
Thanks a lot
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You should also follow the GATK best practices, there are plenty of tutorial that will walk you through this WES analysis and germ line associated mutations.
Best Practices Workflows – GATK (broadinstitute.org)
WES analysis is fairly straightforward that includes trimming the unwanted bases in sequencing results, align them against the reference genome, check for alignment score/errors, check for alignment orientation, look into mutations and annotate them. Every step is documented, and in case you run into problems, BioStars is your friend.
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Hi everyone,
Let me introduce my data:
I am analyzing the single-cell RNA seq dataset. I'm gonna find the differential expression (DEGs) from different conditions in each cell type.
In addition, I'm working with Seurat's pipeline. My data is not suitable for pseudo-bulk DEGs analysis, therefore, mixed-model (MAST) is now my choice!
My question is, why do we need to use the normalized data (Scran-normalized, Log-normalized data) as the input of the MAST test, although the MAST test itself has the normalized method for count-depth (by cellular detection rate - CDR)?
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I just wanna update that I have the answer to this question. Anyone interested in this question can discuss it further.
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I am working with tagseq data that I am aligning to a reference transcriptome of an organism. I used several approaches to produce a transcriptome: using Braker annotation pipeline (with reference genome and RNAseq data), Maker annotation pipeline (also with reference genome and RNAseq data) and de novo SPAdes RNA assembler (with RNAseq data only). Braker showed much higher Busco scores for annotated transcriptome than SPAdes assembly (so did Maker). However, when I align tagseq reads to the Braker or Maker transcriptome I get less than 20% of reads alignment rate. When I align the same reads to SPAdes assembly, the alignment rate is ~80%. This tells me something is wrong with the annotation (regardless of the tool - Braker or Maker). Has anyone run into a similar problem or has ideas why I am getting such a different results for predicted vs assembled transcriptomes?
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Annotated transcriptomes are based on reference genome and RNAseq data, which may lead to a more refined set of transcripts. Reference bias can result in misannotated or missing transcripts, while SPAdes assembly does not rely on a reference genome, potentially capturing a broader range of transcripts. Alternative transcripts may be more comprehensively captured by SPAdes assembly. Intron handling can lead to more fragmented transcripts, while transcription noise may filter out low-expression or noisy transcripts, resulting in a cleaner but less comprehensive transcriptome.
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How can end-to-end workflow automation be achieved for cloud-based machine and deep learning pipelines?
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Here I provided a comprehensive approach to performing E2E automation. Initialize automation by defining the requirements of your ML/DL-based pipeline. Develop models and train large data sets by storing them in secure cloud-based data lakes. Deploy and monitor the real-time insights.
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As OCT creates many downstream issues in the RNA analysis pipeline, has anyone tried thawing OCT tissue (smallish pieces) in prechilled (-20C) RNALATER-ICE? Since OCT is water soluble shouldn't the RNAlater remove most of it (provided you have at least 10 volumes) and still relatively maintain RNA integrity (by also increased extraction efficiency?)
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We need canals instead of using tubes. The curved canals and stoppers could make changes on waters regime to decrease the speed of the water from topsides to the downsides. In Iranian ancient methods, we used the an ancient canals under the ground that was called Qanat. This means, changing directions with another smaller canals could reduce the speed and the water flows from topside to the downsides
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I am new to understanding the transient and steady state analysis of the natural gas pipeline grids. Are there any articles/textbooks that can be suggested which explain about the steady state and transient nature, the gas flow differential equations and how to discretize them?
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A transient state is where the flow of gas changes with time, but a steady state does not. However, one must also account for STABLE and UNSTABLE steady states as well. A stable steady state is one in which the gas flow will always return to its original state after a perturbation, but an unstable steady state is an example of gas flow which does not, but effectively diverges. A mathematical example of a STABLE steady state is a STABLE NODE or a STABLE SPIRAL and an UNSTABLE steady state may be illustrated by an UNSTABLE NODE, an UNSTABLE SPIRAL, or a SADDLE POINT. There are many text books that discuss such concepts, but Jordan and Smith is a good start regarding how to plot the phase diagrams that contain such nodes, spirals, and saddle points. There are also countless Physics books that will discuss the fluid dynamics aspect of the subject, such as Bernoulli's equation for fluids and gases flowing through pipes, but I am unsure of the best ones to cite here myself as I am not a physicist.
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Hello Researchers,
To conduct fracture toughness tests for pipeline material how do you machine specimen using pipelines with small thicknesses (ex 7mm)?
According to ASTM E399, how do you satisfy the ligament length condition with a smaller specimen?
Thank you
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hey guys, I'm working on a new project where I should transfer Facebook ads campaigns data to visualize in tableau or Microsoft power BI, and this job should be done automatically daily, weekly or monthly, I'm planning to use python to build a data pipeline for this, do you have any suggestions or any Resources I can read or any projects similar I can get inspired from ? thank you .
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Creating a data pipeline to automatically transfer Facebook ads campaigns data into Tableau or Power BI using Python is a great idea. Here's a high-level outline of the steps involved and some resources to get you started:
1. Data Extraction from Facebook Ads: Use the Facebook Graph API or a library like `pySocialWatcher` or `facebook-sdk` to fetch data from your ad campaigns. Facebook provides extensive documentation for their API.
2. Data Transformation: Clean and preprocess the data as needed. You might need to reshape it to fit the requirements of Tableau or Power BI.
3. Data Storage: Store the data in a database or file system for easy access and retrieval. You can use databases like MySQL, PostgreSQL, or cloud-based options like AWS S3, or even CSV files. Oracle provides free Express edition database for educational purposes.
4. Automation: Schedule your Python script to run automatically on a daily, weekly, or monthly basis. You can use tools like `cron` (for Unix-based systems) or Task Scheduler (for Windows) to set up automated runs. If you build ETL using Informatica, it has built-in scheduler as well
5. Integration with Tableau/Power BI: Use Tableau's or Power BI's data connectors to import data from your storage location. Both tools provide options for connecting to various data sources.
6. Data Visualization: Create your desired dashboards and visualizations in Tableau or Power BI using the imported data.
7. Deployment: Deploy your pipeline and dashboard to a server or cloud platform for continuous automated execution and accessibility.
For resources and inspiration:
Facebook Graph API Documentation: Start by exploring Facebook's official documentation for the Graph API to understand how to fetch ad campaign data.
Facebook Graph API Documentation
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Due to low flow velocities, there are chances of water and deposits separating in the crude oil pipelines with substantial BS&W content which might leads to corrosion in CS pipelines. Is there any literature specifying guidelines for the minimum flow velocities available?
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Dear Dr. Sharad Londhe ,
I suggest you to have a look at the following, interesting paper:
Corrosion of multiphase flow pipelines: the impact of crude oil
Zi Ming Wang and Jian Zhang
Corrosion Reviews, vol. 34, no. 1-2, 2016, pp. 17-40.
and at the answer of Dr. Henrique Pizzo, at a similar question presented in RG at:
My best regards, Pierluigi Traverso.
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I need help modelling horizontal BNWF with axial, transverse, and vertical (bearing & uplift) springs and spring damper at the ends to simulate connectivity.
I want to know how I can model these on to the beam and assuming the pipeline segment is 1 kilometer in length, at what intervals should the soil springs be applied? Can we assign line springs in OpenSees?
Thank you
P.S I would like to validate my results through this paper "Seismic risk assessment of buried steel gas pipelines under seismic wave propagation based on fragility analysis - Vahid Jahangiri, Hamzeh Shakib" - DOI 10.1007/s10518-017-0260-1
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Hi
Here is one approach to model a horizontal beam on nonlinear Winkler foundation (BNWF) with axial, transverse, and vertical springs in OpenSees:
1. Discretize the 1 km long beam into elements (say 100 10m long elements).
2. Use an ElasticBeamColumn element for each beam segment.
3. Attach zeroLength elements to each node:
- zeroLength in local x-direction for axial soil springs
- zeroLength in local y-direction for transverse soil springs
- zeroLength in local z-direction for vertical springs
4. Use a Parallel material to combine the elastic behavior with a Bilin/Quad nonlinearity for each spring.
5. Apply spring properties like stiffness, yield strength, post-yield stiffness.
6. For damping, attach zeroLength elements with a ViscousDamper material at the ends.
7. Apply restraints and prescribed displacement to beam ends to simulate boundary conditions.
8. For load, apply point loads, prescribed displacements, or ground motion acceleration to the model.
The spacing of the soil springs depends on the desired discretization accuracy. A spacing of 5-10m would likely be reasonable for this length of beam.
This assembles a beam on springs system with nonlinear material models and damping to capture soil-pipeline interaction effects under dynamic loading. The zeroLength elements conveniently allow applying 1D spring-damper behavior between nodes.
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I am looking for information or a database for recording repair, inspection and failure costs of gas pipelines.
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Thank you brother.
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The end of the HCP-MEG pipeline has cifti files that are already parceled out onto the Yeo 2011 resting state networks. However, the cifti files just have 107 spatial points, I cannot find what number correlates to what part of the Yeo parcellation. Does anyone have the answer so I can see what index is related to what part of the Yeo parcellation?
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Thanks! I'll check it out. P
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When I use the DAMASK pipeline in DERAM.3D software, I do not know where the grain orientation corresponds ? And what orientation of the grains corresponding to the '.txt ' file I added through the ODF window ?
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probably the unknown phase corresponds to unindexed points. you need to clean the data until all points have orientation and phase information before setting up a simulation
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RNA from soil will be isolated with Qiagen kit, sequencing will be fine with Illumina 2x150nt.
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I am looking for a way to predict Transcription Start Site (TSS) in Aedes genome, Is there is any bioinformatics software or pipeline to predict TSS from genome sequence or a gene
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To analyze Aedes genomes, DeepTSS (https://github.com/etirouthier/DeepTSS) may be trained.
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Hi everyone,
My project is about the evolution of chemosensory genes in Hawaiian Drosophila. My data is already assembled and masked. I'm wondering which gene annotation pipeline is best for my project? Some people recommended MAKER. Is this the common pipeline that every use? This is my first time doing gene annotation so any advise is much appreciated. Thank you in advance!
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Hi Roshima, thank you for your response! I'm actually using MAKER since Drosophila is eukaryotic. And you're right, MAKER takes a very long time to run. I got 1 species down and many more to go. I'm happy to answer any questions you might have for MAKER as it's a very complicated process.
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Hi all,
I'm busy building a shiny analysis pipeline to analyse protemics data from mass spectrometry, and I was wondering what the exact difference is between the terms Over-represented, and Upregulated. Can they be used interchangeably? Is one more appropriate for RNA or proteins?
Thanks,
Sam
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I would extend that and say we really need to be careful using upregulated. To me, that means the expression of the protein is increased, so there is a fundamental change in the amount of protein quantified as a result of that. I'd suggest we use the term increased (or decreased) abundance when quantifying the protein, unless we have clear evidence to say otherwise. There are a lot of reasons protein quant differs between samples, and it's not always due to expression level changes. I agree you will find such terms used interchangeably, that does not mean it's correct, or a good idea.
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Hello world,
I am a researcher from India. Currently, Pursuing my Ph.D. in Marine Genetics from CSIR-NIO, India.
I want to develop a pipeline to analyze the raw DNA Sequences(WGS) using R or Python or Linux or Pearl language.
If anyone is interested, it will immensely help me.
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Early leak detection in an offshore hydrocarbon pipeline is critical for ensuring the safety of personnel and the environment. However, it is challenging to achieve effective leak detection without false alarms, as a variety of factors can cause false alarms, such as changes in temperature, pressure, or flow rates, as well as instrument malfunction or even marine life interference.
Several technologies are available for early leak detection in offshore pipelines, including acoustic, thermal, and optical sensors, among others. Each technology has its strengths and limitations, and the most effective solution may depend on various factors, such as the pipeline location, operating conditions, and type of hydrocarbon being transported.
One approach to minimizing false alarms is to use multiple sensors and incorporate them into a comprehensive leak detection system that can analyze data from different sensors and cross-check the results to reduce false alarms. Additionally, regularly testing and maintaining the sensors and system can also help to minimize false alarms and ensure that the system is functioning effectively.
Ultimately, achieving effective early leak detection without false alarms in offshore hydrocarbon pipelines requires a combination of appropriate technology selection, system design, and regular maintenance and testing to ensure optimal performance.
Please elaborate on your opinion on it.
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I'm not quite sure about your principles in this area, but I can give you some advice and give it a try using magnetic field detection.
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Due to the constraint of sample, I cannot re-collect the leaves from a genotype that was used for NGS analysis (can only produce draft genome) before. To improve that assembly, can I use the NGS data generated from another genotype (same species but apparently have high heterozygous rate compared to the old one)? If so, please advise for appropriate tool/pipeline and papers dealing with the same issue.
With my appreciation.
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Combining sequence datasets from different genotypes can potentially improve genome assembly quality, especially for regions that are highly variable or difficult to sequence. However, there are several challenges that need to be considered when combining sequence datasets from different genotypes:
  1. Genome complexity: The genome complexity and size can vary significantly among different genotypes, which can affect the quality and completeness of the genome assembly. It is important to ensure that the combined datasets cover the entire genome and do not introduce bias or gaps in the assembly.
  2. Differences in sequence quality: The sequence quality and read length can vary among different datasets, which can affect the accuracy and resolution of the assembly. It is important to carefully evaluate the quality of each dataset and perform quality control measures to minimize errors and artifacts.
  3. Polymorphisms and variations: Different genotypes can have variations, such as SNPs, indels, and structural variants, that can cause challenges in the assembly process. These variations can create complexities in the assembly, such as chimeric contigs, and can also result in incorrect or incomplete assemblies. Special consideration should be given to these variations, and bioinformatic tools such as haplotype phasing and polishing should be used to resolve them.
  4. Computing resources: Combining sequence datasets from different genotypes can increase the computational requirements, especially for large and complex genomes. Sufficient computational resources, such as high-performance computing clusters, are required to process and analyze the datasets efficiently.
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I want to investigate about flow rate changes inside a pipeline in a domestic area, I have searched for the amount of flow rate changes in the pipeline, but I have not found any paper on this subject.
If someone could introduce a paper or chapter of a book on this subject, I would greatly appreciate it.
#flow_rate #pipeline
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The range of flow rate changes inside a pipeline in domestic areas can vary depending on factors such as the size of the pipeline, the pressure of the water supply, and the demand for water in the area.
However, a common estimate for the flow rate range inside a domestic water pipeline is between 1-15 gallons per minute (GPM). This range can vary depending on factors such as the diameter of the pipe and the pressure of the water supply.
Some relevant resources that may provide more information on this topic include:
  • American Water Works Association's Water Distribution Systems Handbook: This handbook provides information on various aspects of water distribution systems, including flow rate, pressure, and demand.
  • Water Supply Systems: Security by Neil G. Parry: This book provides an overview of water supply systems, including information on the flow rate and pressure in pipelines.
  • Pipe Flow: A Practical and Comprehensive Guide by Donald C. Rennels: This book provides information on the flow of fluids in pipelines, including factors that affect flow rate.
I hope these resources are helpful in your investigation.
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I've been trying to know more about bioinformatics pipelines for whole genome shotgun sequencing data to use for the samples of animal fecal microbes diversity and identify pathogenic microorganisms (both of DNA and RNA).
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Dear Dr Abhijeet Singh, thank you so much.
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what is the conditions of flowrate in pipelines of crude oil for wax deposition.how to increase or decrease the flowrate to remove wax from pipelines of crude oil. give me the formula for flowrate.
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I believe these may vary depending on the crude oil properties, ambient environment and pipeline parameters. There are some formulas in the literature. I encourage you to do a search and study them. Better to perform your own experiments if you can.
Let me know how you get on as I am working on a similar topic.
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Hello, someone can help me with information about technology, device or methodologies for inspection, monitoring and repair of damage to pipelines located in subfluvial crossings, pipe installed under a water source (River usually) with difficult access
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I had little experience and no major spills or problems, but some training that might be helpful. Normally, buried pipes of high quality are not going to fail unless exposed or damaged by some activity. Streams and rivers can change location through time. Streams with excess sediment often aggradation, burying pipe deeper. Clean water such as below dams have little sediment, so they typically degrade (entrench), which can expose pipe. Stream channelizing or dredging activities also are used to deepen channels, and could damage pipes if not properly located and protected. Dr. David Rosgen has a paper on cross vanes and J hooks, as instream channel structures of drop rocks or suitable boulders used to manage near bank stress and help armor channel in series from excessive degradation. Some pipe installations may have installed a bipass channel during installation, that might be used to divert the stream or river again if flows are not too high. Hopefully there is a way to emergency shut off pipes transporting hazardous materials or fuels. In some instances, daming the channel and pumping flow around to bipass section might be possible. It is important to develop an emergency action plan in case of accidents or damage from humans, or natural events as floods, earthquake, etc. If the pipe becomes exposed due to channel shifting or degradation, there are probably some channel structures that properly installed would aggradation and channel and re-bury the pipe. Some hydraulic engineers and hydrologists may have this type experiences or can offer some possible courses of action. In channel work, even if dewatered has the potential for spillage, so shutting off pipe and pumping contents out may be needed before fixing. In case of hazards or spills, having emergency plans include downstream notifications of water users or communities may help minimize effects. Inspections may be visual or water sampling specific to pipe contents, chemical, water sheen, perhaps fecal coliform if wastewater, color, smell, etc. Most pipeline companies probably have individuals that know how to fix leaks or breaks. Separate companies may also be needed to address chemical spills with absorbants and quick containment methods for smaller streams and maybe rivers. A downstream river search may offer some ideas on where access and spill containment may be more effective.
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Greetings everyone. I have a png with highlighted areas and I need to convert it into a shapefile with all the pipelines as polygon features. Any help is appreciated.
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Oh, it is easier... The blue, linear polygons that are overlaid on the streets of Jakarta are available here: https://siga.jakarta.go.id/uploads/file_shp/palyja.zip
Download it, unzip it, and you can open in QGIS/ArcMap as it is a simple polygon-type shapefile.
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Hello Expert
Can Anyone suggest the subareal debris flow impact on oil and gas pipeline?
Hydrodynamic loading or debris flow hazard interaction with pipeline?
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You may refer to the article attached to this reply.
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Hello,
I am rather new to the computer aided engineering & design domains and are currently learning the basic techniques how to model, simulate and post-process a model. I learned that the typical pipeline seems to be modelling in CAD -> generating Tet-Mesh -> Simulation using FEM -> Post Process. For design changes, the pipeline is repeated.
Recently, I stumbled across the isogeometric analysis (IGA) method initially proposed by Hughes et al. [1] in 2005, which allows for FEM-like simulation in CAD. This relieves engineers from meshing that can account for up to 80% of development time [2] and shortens the design pipeline/cycle.
Now, many years have passed since 2005 but still the workhorse of computational engineering projects seems to be the FEM. So, I am curious why is IGA not more common in the industry, while it has so much potential? In order to better understand why the situation still is what it is, I would like to read about your opinions.
Lets boil it down to 2 questions:
1) Why is the IGA not more common in the industry?
2) Is the IGA eventually going to replace the FEM?
I would very much appreciate to read about your experiences and opinions :)
Best regards,
Daniel
[1] HUGHES, Thomas JR; COTTRELL, John A.; BAZILEVS, Yuri. Isogeometric analysis: CAD, finite elements, NURBS, exact geometry and mesh refinement. Computer methods in applied mechanics and engineering, 2005, 194. Jg., Nr. 39-41, S. 4135-4195.
[2] COTTRELL, J. Austin; HUGHES, Thomas JR; BAZILEVS, Yuri. Isogeometric analysis: toward integration of CAD and FEA. John Wiley & Sons, 2009.
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The issue of "verification, validation, and uncertainty quantification" is fundamental to the real-world application of numerical methods to critical applications. ASME has published has published standards for solid mechanics (VVUQ 10) as well as fluid mechanics and heat transfer (VVUQ 20). There are additional VVUQ standards that build upon these for specific needs, such as Nuclear Power (VVUQ 30) and Medical Devices (VVUQ 40). There is one under development for Machine Learning (VVUQ 70) that has nothing directly to do with 10 or 20.
The point is, there is lot that goes into engineering tools before they are accepted for engineering applications. Once it's in the "engineering" world (as opposed to "in development"), it must be good enough to be widely used without the dev team or algorithm designer providing any feedback or guidance. This is part of the issue -- as other have already answered, there are issues of quality control with respect to the use of the software tools.
And no, absolutely no, meshing is not 80% of the time in using FEM. That was vaguely true back when one did manual meshing back in the early 90s for more complex models, but it's not true now. Your question is based on an incorrect premise ... and that is why there is not a market-based drive to make the change to an IGA-pure method you hypothesize.
Novelty has it's place in peer-reviewed work. It's a starting point. You seem to be citing just a single set of authors instead of spending a few minutes looking beyond that using RG or Google Scholar. The thing is, IGA is essentially FEM, just taking it from a different angle (no pun intended). ( )
"The goal of integrating computer aided design (CAD) and finite element analysis (FEA) has led to a new computational method called Isogeometric Analysis (IGA). Its main idea is to use the same mathematical description for the geometry in the design (CAD) and the analysis (FEA). Much of the recent research on isogeometric analysis uses Non-Uniform Rational B-Splines (NURBS) as basis functions, as this geometrical representation is the most widely used in engineering design systems. It has been shown that NURBS-based finite elements are very well suited for computational analysis leading to qualitatively more accurate results in comparison with standard finite elements based on Lagrange polynomials. Due to these motivating results, NURBS-based finite elements are currently implemented into LS-DYNA."
Overall ... IGA techniques are growing in popularity and are being folded into existing computational platforms, just a BEM (boundary element method) techniques have. It's not a question of "one size fits all".
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I have the scRNAseq data sequenced by BGI, which can be processed by cellranger. but the result always show "Low Fraction Reads in Cells" as the fig showed
does any know the reason, I also tested my pipeline with 10X test data, result is ok
is there with any mistake I made or some bug between BGI and cellranger
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Try Kallisto bustools.
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is there any bioinformatics based tool for annotation of 16s rRNA?
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There are some great tools for 16S datasets, depending on whether you're looking for ASV-level results (dada2: https://benjjneb.github.io/dada2/tutorial_1_8.html) or OTU-level results (mothur: https://mothur.org/wiki/miseq_sop/).I recommend reading about these to see which one best suits your needs. Both of these tools will create an object that will tell you which sequences are in which samples, and an object that will tell you the taxonomy of the sequences. These objects, and your metadata object/csv file, can be used in downstream diversity analyses with R packages suited for 16S data. These packages include phyloseq, vegan, and microviz. Here are two more links which may be useful: https://mibwurrepo.github.io/Microbial-bioinformatics-introductory-course-Material-2018/set-up-and-pre-processing.html#otu-or-asvs-or-sotus
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Is there a solution for liquid hydrogen and gas hydrogen transmission line leakage?
What is your suggested software for simulating the hydrogen transfer process in pipelines?
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Hi,
I’m more a specialist in Fuel Cell Air supply.
I can give you only a general statement for pipelines with gaseous H2:
If the right steel alloy is used, diffusion of H2 will be no issue.
As liquid H2 has a temperature of -253 °C it is very questionable to use a pipeline.
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I need to make publication ready figures from the network data generated by MENA pipeline. R package is also okay!
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Dongmei Wu which package, can you please provide me the code
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The pipeline conveys liquid from a high peak and then down. If the fluid is discharged by gravity from one side of the pipe, is it possible to crumple the pipe due to the negative pressure at the tip of the peak? How can you calculate the pressure difference required to destroy the pipe at the top?
By draining how much volume of fluid at the bottom of the peak, the pipe may be damaged in the peak?
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The pressure of a liquid won't go below it's vapor pressure. If it drops to the vapor pressure, it will start to boil (if it's a mixture, it will vacuum distill due to differences in boiling pressure) and the pipe will form a vapor pocket. As you remove more liquid, the vapor bubble will get bigger but its pressure won't change much.
There are methods for calculating collapse pressure and full scale testing is also commonly performed. Because the lowest fluid pressure is 0 Pa absolute, collapse of steel pipe is usually only a problem when the outside pressures are high, like in a subsea environment.
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Soon I will have to analyze some ATAC-Seq data, I was evaluating the pipelines currently available ... that it is simple to install (maybe conda) and to use ...
I was considering:
Or
Or
Any experiences or suggestions?
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Maybe you want to start reading this paper :)
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Dear all,
I am looking for a user-friendly pipeline for metagenomics analysis using COI (Cytochrome oxidase I) as marker. I have tried some of them based on python and computed by docker but is not enough clear to be used with students. Could anyone recommend me any alternative?
Thank you in advance.
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The link posted above is useless and it does not relate what was asked in the question.
Try:
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I'm beginning a research paper on the Eastern Mediterranean Pipeline's effect on the economy of Israel, Greece, and Cyprus. What would be a good way to phrase this question?
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If i may provided the following suggestion: What will be the economic impacts of the planned Eastern Mediterranean pipeline on Cyprus, Greece, Israel and North Cyprus?
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Dear all,
I have been doing research on the leak detection of pipelines for some time. I did the simulations with simcenter software. But unfortunately, I tried to detect the location of the leak using Kalman filter in different ways, but it is not possible. Is it possible to guide me? Is it possible to send me the MATLAB code so that I can try on my own water pipelines and simulations?
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Richard Fenner and Steve Mounce have done work using Kalman filters for leak detection in water distribution networks Seyed.
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I have completed my bachelors and masters in the medical field. I don’t have a great CGPA because my University doesn’t give much marks to our students. 72% is the highest in my field (Gold medalist), and I have 70.625% (Silver medalist). How do I pitch this point to the Universities?
Also I have 5 PubMed indexed publications (with 6 more in pipeline)
My IELTS score is 8 overall (L 8.5, R 9, W 7.5, S 7.5)
Do I have a shot at Ivy League institutes for a PhD?
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You still have a good chance in other universities around the world, for your rank is so good. Regards.
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I have RNA that is going to be used on the ONT (Nanopore) technology pipeline and my RNA is too dilute. Is there a protocol to dry/pellet the RNA in solution and then re-suspend the RNA in at a lower volume?
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The above answer is acceptable.
Here is my protocol:
1. Obtain volume of RNA
2. Add 1/10th volume 3M sodium acetate and 1/100th volume glycogen (I typically use 10mg/mL stock)
3. vortex
4. add 3 volumes 100% ethanol (only use 1 volume isopropanol if you are gel extracting the RNA or your total volume would exceed 1.7mL)
5. precipitate overnight at -80oC (for small RNAs, you need overnight incubation)
6. spin down RNA at max speed, 4oC for 35 min.
7. Wash the RNA pellet with 3 x 1mL ice cold 80% ethanol washes. make sure during each wash, you vortex pellet such that the pellet is released from the wall. spin down for 5min at max speed.
8. Carefully decant pellet by removing ~0.8mL with a p1000, pulse spin, then ~200uL with a p200, pulse spin, and then vacuum up remaining liquid with a p10.
9. air dry pellet for 1-2 minutes. Do not over dry or your pellet will be difficult to redissolve. If you dried the pellet perfectly, after addition of water of TE, you'll see the pellet "dance" at the top of the liquid surface as it is rehydrating.
10. add buffer of water to reconstitute pellet. Let sit at room temp for 10 minutes. Do not pipet the pellet during this incubation because it could stick to the tip. after 10 minute incubation, pipet a few times and check if pellet is dissolved. If not, let the pellet sit longer at 4oC and check again.
Alternatively, you can use Zymo's RNA concentrator kits to get the volume smaller. Just note some kits have concentration and RNA size limits.
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I am a young bioinformatics student, want to have clues for my project pipeline. hints and expert answers are welcome. THANKS
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I'd start with inferring the amino acid sequence and then BLAST it against proteins of known function. That way you can leverage what is known about the homologous, known proteins to build your starting hypothesis about your unknown protein. You can then design more targeted experiments to test your hypothesis.
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I want to calculate Steel pipeline corrosion rate in different conditions, so Which software is best for estimating of pipeline corrosion rate?
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Dear Dr. Meysam Najafi Ershadi,
The COMSOL FEM package can implement modeling of corrosion growth on pipeline steel.
Hope it is helpful for you.
Best,
Guojin
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Hi, I am new to bioinformatics. My project involves Next-generation sequencing to look at differential gene expression of treated and untreated cells. I found that many papers have different methodologies. Some paper uses Linux but I am not good at it. Can anyone suggest a standard pipeline that uses R studio on Windows PC? Your valuable suggestion will be greatly appreciated.
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Definitely check out the LatchBio RNA-seq analysis pipeline. It's super easy to use and cloud-based which I've found convenient.
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Is it possible to calculate with following given data? outlet temperature and pressure of steam, capacity of boiler, Diameter of pipeline.
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Probably... but the accuracy of the results depend on the assumptions. For example, the capacity of the boiler only matters if it was accurately designed and operated as prescribed. If the manufacturer doesn't know what they're doing (and some don't) or the boiler is operated off-design, then the design point won't be meaningful to the conditions in question. You also need the inlet steam conditions and the steam flow. You might want to read ASME PTC4. While it is a strange and convoluted document, it does describe how to estimate a variety of things based on what you do know instead of what you wish you knew. For example, you would like to know the composition and flow rate of coal (which varies continuously and is extremely problematic to measure) plus the mass flow rate of combustion air (or the mass flow rate of the exhausting products of combustion), which is also very difficult to actually measure. You should also read several test codes (ASME and ISO) on flow measurement, which is a lot harder to do accurately than most people realize. Sticking a probe into a flow or clamping on an acoustic flow meter, no matter how expensive, doesn't mean that the results aren't garbage. Post a picture and labeled schematic drawing of your system.
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I am pursuing Ph.D. on anthropogenic impact on fluvial environment. This is my last year my work is almost complete. Can anyone walk me through the process of pursuing PDF in India or preferably abroad? I have one international publication in springer on water quality and two other are in the pipeline on river migration process and anthropogenic impact on rivers.
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Hello.
funded-PDFs
This is done with the Ctrl-F key
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Hello everyone,
If I have a sequence of a protein in fasta format (or any other), how can I find which structures exist for the exact match or similar sequences programmatically? Is there any Python package that can do it?
PS: I am aware that you can do it with web servers like uniprot but what I look for is mostly a command-line tool that I can integrate into a pipeline.
Any help is appreciated.
Mustafa
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Hello,
While performing blast, you can choose protein data bank as the search set. It will give you the pdb identifiers in the 1st column of the output. Hope this helps.
Best,
Aysima
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I have to simulate a pipeline which is API 5L X60. I've been searching in the literature and I didn't find anything.
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I still looking for the answer T_T
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I'd like to ask if anyone can provide me with any papers or information on this subject.
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Dear Amrit,
All drinking water distribution systems, no matter how complex, can be handled by EPANET.
Regards
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Please, I am looking for dataset (that has flow, heat. temperature, knock, pressure, and any other parameters data in oil pipeline) that I can use for the purposes of leakage detection and its location using machine learning.
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I need to evaluate the eigen frequency of pipeline using abaqus. adding deadload of fluid in the pipe is problematic for me. during frequency analysis no load is allowed to act.
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You can easily make it in Ansys APDL. Prepare a geometry with proper dimensions including fluid density and apply boundary conditions. you can get easily mode frequencies
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as i had done this in ansys so how can i verify my result as my project head said to verify whether it is correct or not please help
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as i had not found any paper in which ansys simulation is done for the underwater pipe if you find can you please refer me
as i had to submit my project@claudio Pedrazzi
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Hello All,
Let's say I have a pipeline connecting to the outlet of a blower. The pressure at the blower outlet and thus the inlet of pipeline is 1500Pa. The pipeline is only subject to major and minor head loss and the loss due to change of elevation. The diameter of the pipeline is constant.
When I calculate the pressure drop along the pipeline, I found the pressure drop is 2500Pa. Meaning to say, the pressure at the end of pipeline is around -1000Pa. Is this possible to happen? Does gas able to flow along the pipeline and flow out at the outlet? What is the impact to the gas and pipeline?
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If the pressure at the end is below the atmosphere means the atmospheric air will flow in. Check your calculation if it is correct either need to increase the output pressure of the blower or change the material or length of the pipe to reduce pressure losses. The height also is a problem, in that case, you may consider erecting the blower at a height, based on calculation, to reduce the pressure drop. If you can specify the application and your situation better, either I or anyone else can give an apt solution.
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Good morning,
Please I have an issue with my run and I need some help.
We did a metagenomic 96 sample run on Minion Mk1B (short-read 16S 400bp amplicons). The run lasted for 72 hours. Output was 9.7 gigabases (FAST5 files are 241GB). After this base-calling was initiated.
After 24 hours, the base calling was only 17% at which we aborted the base calling to do it on our server.
After 4 days now and only less than 20% is done. Why is it taking so long? We are using guppy v5.
What is the expected output size for such runs?
Does analysis usually take this long?
Is there a time limit by which we should stop the runs?
Thank you in advance.
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In my experience, yes, it takes many days to do base-calling with the guppy base-caller. However, it depends on what guppy version you used; if you use the guppy CPU version it will be much slower compared with the GPU version. The number of threads you used also affects the base-calling process.
I think no time limit for this. You just need to wait until 100% to get all your data converted to FASTQ by the program, or, you may need to adjust the base-calling parameters or change the program version and re-run the guppy base-caller to make it faster.
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Dear scientists
Our team sequenced the human whole-genomes for breast cancer genes analysis. We could manage to generate up to the VCF files. Now we want to annotate the data and do the KEGG pathway analysis the find out the networking of the genes. Anybody can show us the necessary pipeline along with the basic tools to solve the problem?
Thanks in advance.
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Dear researcher variant annotations can be produced by HaplotypeCaller available in gatk suit. Also you can try Mutect2 or VariantAnnotator. And for pathway analysis try KEGG Mapper.
BTW I have lot of exprience in WGS analysis, if you are interested we can start a collaboration for this work.
Best Wishes
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How do i go about simulating a pipeline network with simscape/simulink to measure parameters pressure and flowrate in case of leakage. Any guidance or tutorials will be appreciated.
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Great question !
I honestly don't know something about simscape/simulink, but from what I know is that to measure the pressure through simulations in case of leakage, I can refer you to an article that got published in "The Institution of Mechanical Engineers" :
It's true that it's applied just for tyre pressure, but since the mechanical fluid equations are generalized for any pressure/flowrate situation, adding to this the Scale's Law; I find that you can get what's important there.
If I might precise more, while conserving the confidentiality of the article, I can say that it might be helpful to know the theoretical equations used in it, the pathway through the Scale's Law to simplify some parameters (which might get adapted to your situation, I find), plus the method they used for simulating the pressure.
What I can say, from my point of view as a student and incoming research intern in this field (your situation especially), is that this article helped me understand the scientific methods used to measure the pressure and simulate it.
I hope this would be helpful in your case, as I'm still a student and not fully experienced in this field, to be honest.
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Can anyone help to check whether the major head loss calculation for the attached pipeline is correct? Kindly advise. Thanks!
Inclined uphill portion:
Length, L= 5.68m
Diameter, D=0.5984m
velocity, v= 17.62 m/s
surface roughness / Diameter, e/D =0.000250668
Re=4.08E+05
friction factor, f =0.0165
Pipeline Inclined angle = 70 deg
So,
Head loss=[ f*(L/D)*(v^2)/(2g) ] + L*sin (70 deg) =6.874042435 m
Straight Horizontal portion:
Length, L= 9.8m
Diameter, D=0.5984m
velocity, v= 17.62 m/s
surface roughness / Diameter, e/D =0.000250668
Re=4.08E+05
friction factor, f =0.0165
Pipeline Inclined angle = 0 deg
So,
Head loss=[ f*(L/D)*(v^2)/(2g) ] =4.276014958 m
Inclined downhill portion:
Length, L= 5.68m
Diameter, D=0.5984m
velocity, v= 17.62 m/s
surface roughness / Diameter, e/D =0.000250668
Re=4.08E+05
friction factor, f =0.0165
Pipeline Inclined angle = 70 deg
So,
Head loss= [ f*(L/D)*(v^2)/(2g) ] - Lsin (70 deg) = -1.917355708m
Total head loss= 6.874042435 m + 4.276014958 m - 1.917355708m
Total head loss=9.232702 m
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Dear Carrie Chang,
Please correct the value of the friction factor f. The exact value is:
f = 0.0161460, instead of f = 0.0165
Also: L*sin(70°) = 5.68*0.939692621=5.337454086 m
Regards
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What is parametric stress analysis for pipeline bends.
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Hi,
Depending on the requirements you have (type of analysis 1D or 3D) :
- 1D piping software like C2 have integrated SIF (Stress Intensification Factor) that's allow parametric design integrating radius, thickness, number of section if it's a miter bend.
- 3D Analysis with FEM software's parametric geometry have to be created using scripting or parametric CAD software like Solidworks or Catia for example can be used and the stress analysis will be done with volume or shell elements depending on the accuracy requirement.
Best regards
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What is the latest pipeline to run the RNA-Seq genomic data ?
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Try tuxedo pipeline II. here is the reference https://www.nature.com/articles/nprot.2016.095
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HI guys,
I have heard many reasons that researchers do not want to move to cloud for their analysis. I definitely see cost being one of the challenges - which is being currently worked out.
With pipelines/workspaces and data available on the cloud- what could be improved for better use of cloud between labs/institutes for genomic analysis.
Mamta
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Dear Mamta Giri,
Take a look at those auxiliary data as well:
Building Terra, the Broad Institute’s Platform for a Collaborative, Scalable Genomics Research Ecosystem for All:
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A research on corrosion prediction in a gas pipeline using artificial neural network is the core interest. This time, an experimental data to model and train the ANN is required. Thanks in anticipation.
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Dear Dr. Nurudeen Sabi ,
I suggest you to have a look at the following, interesting web site regarding a pipeline safety project, available at:
My best regards, Pierluigi Traverso.
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KH9 Hexagon images come in parts as (a) and (b), without any georeference. Manually georefrencing two parts in ArcGIS is giving a considerable error. The Heximap pipeline is not working with the images freely available from USGS as Declasss2. How do i stitch those images for further processing?
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This article may help you "Automated Processing of Declassified KH-9 Hexagon Satellite Images for Global Elevation Change Analysis Since the 1970s"
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The main goal behind this question is extracting the best practices on how to establish a Data Science / IA Project.
Anyone would be generous to share with us the set of tools or even a boilerplate that may help or guide anyone working in the field and applying data science & IA to any domain.
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It very depend on dataset that are you going to used. Please specify the task tha are you going to solved. The preocess quite straight forward.
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Hello,
I am new in this field. I am doing metagenome analysis with shotgun reads. All reads are single ended. DNA was obtained from airways of human. I just want to find taxon abundances in the samples. Then I will predict the diversities and core microbes.
My mapping results are terrible. How can I handle bad mappings?? OR should I change the tools that I used the analysis?? Which tools are more accurate or sensitive for microbiome analysis?? I need any suggestions, please!
I followed this pipeline:
  1. Assembly was done using Megahit
  2. Short contigs (<200 bps) were removed using prinseq
  3. Read mapping against contigs was performed using BWA
  4. Similarity searches for GenBank, KEGG, , eggNOG were done using Diamond
  5. Binning was done using MaxBin2
You can find my mapping results in the attachment.
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Dymphan Gonsalves Thank you very much, your answer is very helpful.
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I need a brief explanation of pipeline flow conditions that the Darcy-Weisbach equation can be applied and how this application carried out?
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On the above question I specifically interest in application of the equation to gas flow
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The area in question has recorded several oil spill events in recent times due to pipeline vandalization of both crude and refined petroleum hydrocarbon products. Depth to water level is about 9 m. Groundwater samples were collected from hand dug wells and motorized boreholes. In both type of wells, dissolved organic carbon concentrations ranged between 15 to 53 mg/L while the redox potential ranged between + 21.4 to + 587.4 mV
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I seem to remember that perchlorates in groundwater can get into that ORP range and perchlorates can be from both natural and man-made sources (rocket fuel and fertilizers -- really natural sources) and their reactivity with organics is low enough that many refractory organics like tannin compounds are stable.
Under anaerobic conditions, bacteria can use organic carbon (non-refractory organics) to reduce the perchlorates. An ORP of about -100 will eliminate perchlorate in bioreactors or in-situ.
If it is perchlorate, that can be a drinking water issue. It can cause health issues.
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With many literatures and tools of bioinformatics to analysis single cell RNA data, I would like to ask if there is a complete pipeline for all the process of the analysis. It includes a downstream steps of co-expression network constructions within R programming.
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Thanks a lot for your detailed reply. i will try that package. keep in touch
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i have a project to do the vibration analysis of underwater pipeline hence i dont know from whee to start and how to do please help
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You should be aware of the widely used document in pipeline industry titled: "DNVGL-RP-F105 Free spanning pipelines". Then ANSYS can be used for a simple beam modal analysis if needed to determine the governing vibration frequencies and mode shapes which are used therein, with due account for the effective axial equilibrium force in the pipeline.
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I will be thankful for you if you share your knowledge with me and suggest the best coating process if we use Nick (Inconel 718) as as inner coating process in oil pipeline.
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Dear Mohammed,
I recommend you to study the literature on NiCrBSi alloys. This is an old and valued system with a lot of information and experience. Also visit this forum:
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Does any one have good pipeline for analyzing bacterial RNA seq data using R? I found many pipelines and tutorials using eukaryotic data, but it is very tough for bacterial sequencing data.
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Try Tinity pipeline.
If your bacteria is a novel, then you can choose de-novo assembly then differential expression.
If reference genome if already there then you can use reference genome base assembly and followed by differential expression.
Downstream analysis you can use EdgeR or DESeq2
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Hello,
I am trying to preprocess DWI data for the first time in order to extract diffusion parameters and to perform tractography. I have watched all the tutorials provided by the Analysis Group (FSL), Andrew Jahn videos on Youtube and I have studied the DTI pipeline. However, I still have questions.
It is not very clear if I should preprocess my T1 data too. I am using it to perform registration with my diffusion images. I know that I should extract the brain (Bet function) but I was questioning about possible others steps I am missing? I am afraid it could bring artefacts onto my results.
Thank you for reading me,
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Yes you should correct your T1 images before doing anything with your DWI. Here are my recommendations, please keep in mind that this varies from person to person but the below mentioned steps I have seen most common in diffusion imaging papers.
1. Fixing the orientation i.e. Moving into standard space or center your brain to (0,0,0). You can use FSL's fslorient2std command to re-orient.
2. Denoising
3. Gibbs ringing correction
4. Bias field correction
5. Skull stripping
In case if your T1 data is not in isotropic voxel you may also need to resample it too.
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Suppose there is a leak in a crude oil pipeline, after which the inlet valve of the line will be closed. However, depending on the length of the pipeline, it may take some time for the current in the ruptured section of the pipeline to be completely cut off. I am trying to calculate the flow rate change at the rupture location of the pipeline. (in my case pipe line length from leak to valve in about 25 km)
Different sources such as "OCS Study MMS 2002 - 033" have presented different equations to calculate the amount of leakage, but the results obtained from these equations in the best conditions calculate the amount of leakage after closing the valve equal to half the volume of the pipeline. It should be noted that none of these equations take into account the slope of the pipeline, which is also based on the events that have been recorded. It should be much less than half the volume of the pipeline. Does anyone have more information on how to accurately calculate the amount of leakage? It should also be noted that due to the very long length of the pipeline, it seems impossible to use CFD model. (I tried fluent)?
Thanks
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Hello.
Although the equations you mention can help outline the approximate extreme leakage, the scenario you have laid out is quite complex and depends on many factors such as: the pipe diameter, length and slope of the flowline, as well as the initial flowrate (velocity and momentum of the fluid), fluid PVT and ambient conditions (temperature and pressure of the system outside of the pipe compared to inside).
You are correct that CFD software is not designed for this type of analysis, in industry I would recommend a transient pipeline flow simulation software such as OLGA or Ledaflow.
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There are many drag reducing agents suggestested for oil pipilines, I would like to know which one is more applicable?
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(co)polymer of higher (meth)acrylate (polymers of higher alpha-olefins) with a hydrocarbon group having from 4 to 30 carbon atoms and a molecular weight of the polymer/copolymer not lower than 4-10(6).
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Dear all,
I'm relatively new to the "ATAC-seq technology", I performed an ATAC-seq experiment using different cell lines (non transformed and cancer cell lines) and recently I received the sequencing (Raw) data.
I will be very grateful if you can share with me tutorials/reviews or useful links in order to analyze my ATAC-seq data (python or R scripts, pipelines.........)
Many thanks in advance
Karim
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In some cases when I use black oil model the software stops solving the problem and warns that the pressure is beyond the range. I activated the slug tracking and problem is solved but when I want to run the pig there is a problem. how can I find out the cause of this error?
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Hi there,
Could you solve your problem with OLGA?
In cases that you receive an error because thepressure or temperature is out of range, you need to extend the range of T and P in your PVT table. You can do it by PVTSim software or Multiflash.
If you’d like you can connect to me to work on OLGA software and solve the problem. I am really interested in
Best regards,
AskarSoltani
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Hi all, currently I am working on Whole Genome Sequencing for some samples. Unfortunately, while performing the mapping process using bwa, the analysis retrieves me an error of
[M: :mem_pestat] skip orientation FF as there are not enough pairs
[M: :mem_pestat] skip orientation FR as there are not enough pairs
[M: :mem_pestat] skip orientation RF as there are not enough pairs
[M: :mem_pestat] skip orientation RR as there are not enough pairs
[mem_sam_pe] paired reads have different names: "E00534:137:H5KC7CCX2:1:1101:3488:1731", "E00534:138:H5KL3CCX2:1:1101:2493:1625"
Previously, I found one solution, suggesting running a repair.sh via bbmap/bbduk software however, I am not sure either I need to trim back the repair file via trimmomatic or just direct to mapping process after the repair/fixed process. Thus, here I would like to ask, what are others solutions that can I use to solve this mapping error and should I directly skip the trimming process via trimmomatic and direct to the mapping process.
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I need Raman spectrums for develop data analytics pipelines to classifying chemical substance using Machine Learning techniques.
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Hello. I would like to cut the surface of pipeline with girth weld to investigate the effect of residual stress on pitting corrosion. I am planning on adding bending force to the samples to make the situation more realistic, and I think I need flat samples to do so. Does anyone know how to cut the samples and flatten them while minimizing the effect on residual stress in the surface? Thanks in advance.
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GO for Abrasive jet machining,
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Dear All,
Which tool/software/script can extensively annotate bacterial genome with lower % of hypothetical protein annotates.
On annotation using PROKKA there are many sites without incomplete annotations. Is there a method/s or pipelines which help annotate such sites.
Any help would be really appreciated.
Thank you
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I agree with prokka too!
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How do we apply fuzzy logic in corrosion under insulation of pipelines?
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Dear Dr. Gabriel Yob ,
in addition to the correct explanation of Dr. Mahmood H. , I would like to add also these references which may be useful to you:
-Prediction for CUI in Piping Systems using Fuzzy Logic with Sensitivity Analysis of Corrosion Producing Factors
Muhammad Mohsin Khan, Ainul Akmar Mokhtar, Hilmi Hussin, Masdi Muhammad
MATEC Web of Conferences 225, 06002 (2018)
-A Fuzzy Logic method: Predicting pipeline external corrosion rate
Maria Victoria Biezma, Diego Agudo Saiz, Gonzalo Barr´on
International Journal of Pressure Vessels and Piping 163 (2018)
-Real Time Implementation of Incremental Fuzzy Logic Controller for Gas Pipeline Corrosion Control
Gopalakrishnan Jayapalan, Ganga Agnihotri, and D. M. Deshpande
Hindawi Publishing Corporation Advances in Fuzzy Systems, Volume 2014, Article ID 203739, 9 page (2014)
My best regards, Pierluigi Traverso.
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Is there any relationship between the tendency of a gas to leak from containers/pipework and its molar weight?
For instance, given smaller molar mass of hydrogen (2.016 g/mol) compared to 16 g/mol for Natural Gas, is it correct to conclude that Hydrogen would exhibit a greater leakage risk when replacing natural gas in utility pipelines when transmitted under the same working pressures?
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Please find enclosed to this message a paper that explains different parameters affecting the transmission of gases.
Best
Duried
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I am performing differential gene expression analysis using the CIRIquant pipeline. Referring to the CIRIquant cookbook, I successfully arrived into this step:
"Usage 3: Differential expression analysis - Study with biological replicates - Step3: Differential expression analysis"
However, there is an EdgeR error occurring (see below). Can someone explain to me what I may have done wrong?
Command used:
CIRI_DE_replicate --lib library_info.csv --bsj circRNA_bsj.csv --gene gene_count_matrix.csv --out circRNA_de.tsv
Log:
[Wed 2021-03-17 22:11:31] [INFO ] Library information: /home/andregabriel/Desktop/CIRI_test/library_info.csv [Wed 2021-03-17 22:11:31] [INFO ] circRNA expression matrix: /home/andregabriel/Desktop/CIRI_test/circRNA_bsj.csv [Wed 2021-03-17 22:11:31] [INFO ] gene expression matrix: /home/andregabriel/Desktop/CIRI_test/gene_count_matrix.csv [Wed 2021-03-17 22:11:31] [INFO ] Output DE results: /home/andregabriel/Desktop/CIRI_test/circRNA_de.tsv Warning message: In estimateDisp.default(y = y$counts, design = design, group = group, : No residual df: setting dispersion to NA Error in glmFit.default(y = y$counts, design = design, dispersion = dispersion, : Design matrix not of full rank. The following coefficients not estimable: treatT Calls: glmFit -> glmFit.DGEList -> glmFit -> glmFit.default Execution halted [Wed 2021-03-17 22:11:35] [INFO ] Finished!
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I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff, star+stringtie+cuffdiff etc. However, among all the pipelines, only the Cuffdiff differential tool gave some genes with significant Q value whereas none others gave DEGs with significant adjusted P-value. So I would like to know from the people who are working with brain samples, what possible ways can be used for analyzing such data? What kind of adjusted P-value and log2fold change do you observe in your routine analysis?? Is there any specific normalization technique or pipeline for analyzing brain tissue samples??
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Hi Simang,
I don't have experience with transcript-level DE analysis. But I suppose I would try it first with a pseudoalignment tool (e.g. salmon, kallisto, sailfish) and then differential expression with Sleuth. For gene level DE, I would use deseq2 or edgeR with the same counts but summarized at gene level.
What is the species you work with? Maybe first make sure it has a good enough cDNA set, if you decide to rely on mapping to transcriptome.
In case you haven't done so already, you should also check PCA plots for gene-level aggregated counts (you can use deseq2 for producing pca plots). Your statistical power might increase if you remove certain outlier samples (e.g. remove "disease" samples which are grouping with control samples).
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Hi,
I am trying to analyse sequences produced using SMRT link from PacBio. My goal would be to produce asvs table and taxonomy as for a normal DADA2 pipeline, but I am struggling finding information about how to use the output sequences from PacBio in any bioinformatics pipeline.
Any suggestions?
P.s. still a newbie! ;)
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I work with genetics and would like to ask if anyone can suggest any (drawing or figure) software tools suitable for making custom figures e.g. of pipelines, molecule interactions, DNA, RNA etc.
Any suggestions are appreciated, Thanks!
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Optimization of hydrocarbon pipeline transportation and allocation using a pipeline network measurement system model
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You could look for articles with the same topics that you're working on in any database. Then, you could identify the journals where those articles were published, and compile a list of related journals. As Princewill Ikpeka recommended, you could use the SCOPUS database, or even the Google Scholar site (some tips here: https://www.youtube.com/watch?v=dc-vKk205c8). However, you always should make a further review of the identified journals, to validate their scientific quality and credentials.
Best regards!
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I am investigating the effect of velocity on severe slugging and this requires a CFD software that can simulate severe slug flow and at the same have the capacity to vary input velocities.
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You can check out some recent papers published by researchers at Cranfield.
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I have a dataset of eeg, sampled from children.
No electrodes attached to eyes area, so i can't use the function "reject data using ICA",
what is the best way to preprocess the data depending my situation?
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thanks!
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In 16s rDNA metagenome analysis, after sequencing data. I want to classify bacteria based on their functions. I am looking for a Pipeline or any software that can do this job?
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Thank you all for your response.
Muhammad Ali The provided reviews are helpful for analyzing the metagenome data but they are not providing the answer to my question. Thank you
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Hi Everyone,
I have acquired some plant hyperspectral images (roots, fruit, leaves) from various environmental conditions and now want to explore the data cubes to detect possible differences and plan to study plant physiology and chemometrics in future. The built-in software with the camera (Specim IQ studio) is not serving the purpose.
Any suggestion for easy-to-use and simple interface software or analysis pipeline for such exploration and making classifier models? Preferably open-source but commercial suggestions are also welcomed.
Many thanks in anticipation.
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Yes, the folder looks like this for a single snap!
I will inbox you as well. Thank you again :)