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For de novo gene prediction in your genome assembly project, AUGUSTUS is a reliable tool. To get started, one can use the following command line. Here, the --species parameter specifies the organism to use as a gene model. In this case, I used maize . The --progress option displays the process. Unfortunately, when you run the command, it uses only one CPU core: AUGUSTUS does not have a built-in parameter to set the number of CPU cores. However, we can leverage GNU Parallel to utilize multiple cores. Check if the parallel is Installed and is in the PATH You can verify GNU Parallel's installation by running the following command in your terminal: parallel --version. It should output as follows. Or you can type dpkg -l | grep parallel   and it should bring If GNU Parallel is not found or installed, you can install it on Ubuntu using the following command: sudo apt-get install parallel Split the main fasta file into multiple files To divide a large FASTA file into smaller, manageable files, use the following Python script. This code splits the file in a "fasta-aware" manner, ensuring each resulting file remains valid. In the code, you can replace the value of "n" with the number of fasta files you need. Check the number of CPU cores The following command can be used to check the number of CPU cores. cat /proc/cpuinfo My server is equipped with two Intel Xeon E5-2609 processors, each featuring 4 cores. This configuration provides a total of 8 cores. To verify cores and threads per core, use lscpu Automate AUGUSTUS on multiple FASTA files in parallel, across “N” CPU cores First of all, we need to configure OpenMPI for AUGUSTUS. To control thread allocation for AUGUSTUS, set the OMP_NUM_THREADS environment variable. This variable determines the number of threads allocated to OpenMPI-enabled applications. To restrict AUGUSTUS to single-threaded operation, set: Run parallel instances of AUGUSTUS. With OMP_NUM_THREADS set, you can now run multiple instances of AUGUSTUS in parallel using GNU Parallel: parallel --jobs N augustus [options] input_files. Replace: 1. N with the desired number of parallel instances (equal to the number of cores, if hyperthreading is not supported), 2. [options] with AUGUSTUS command-line options 3. input_files with your input FASTA files. To maximize efficiency, you may set the optimum number of parallel instances; for example, set N to the number of cores, considering: 1. Single-threaded operation (OMP_NUM_THREADS=1) 2. No hyperthreading support. In my case, with 8 cores and single-threading: parallel --jobs 8 augustus [options] input_files. Now to automate, set an input directory variable (INPUT_DIR) and an output directory variable (OUTPUT_DIR), and assign them the path to the folder that contains all split input files and the path where the output files are to be created. Now 8 parallel instances of AUGUSTUS  can be run using the following command: Here, the {}  grabs each input file (each one from the group of split files) mentioned in "$INPUT_DIR"/subset_{1..8}.fasta . Each parallel job is individually redirected. Combine the output files: The  '>' "$OUTPUT_DIR"/{/}.gff3  will create individual output corresponding to each AUGUSTUS  task, and all the split output files need to be combined. This can be done by: The complete program You can find the complete program here.

Specialized Training Program on Arka Fermented Cocopeat and Soilless Cultivation of Vegetables ICAR-Indian Institute of Horticultural Research, a premier institution under the Indian Council of Agricultural Research, is organizing a specialized with Arka Fermented Cocopeat The training is a unique opportunity for entrepreneurs, startups, and enterprises looking to harness innovative horticultural technologies. This hands-on program will guide participants through the production of Arka Fermented Cocopeat, a sustainable substrate ideal for soilless cultivation, which has proven to be highly effective in horticulture. The training will be conducted by esteemed experts, including Dr . G . Selvakumar and Dr . D . Kalaivanan , both Principal and Senior Scientists from the Division of Natural Resources. Participants will gain valuable insights into practical applications, with the offline sessions covering both theory and practical demonstrations. Additionally, an online option is available for those who wish to attend remotely, focusing on theory sessions. Training Program Details Key Details : Venue : Video Conference Hall, Admin Building, ICAR-IIHR Date : September 20, 2024 Application Deadline : September 19, 2024 Offline Training Fee : ₹2000 (9:00 AM to 5:30 PM) Online Training Fee : ₹1000 (9:00 AM to 1:30 PM) Organized by BESST-HORT , the Technology Business Incubator of ICAR - IIHR , this program is a critical step for those aiming to develop viable skills in horticultural innovation and entrepreneurship. The training is supported by NIDHI-TBI and the Department of Science and Technology, Government of India. Register now to secure your spot in this transformative training session! Visit BESST-HORT for more information and registration details. Apply at: https://www.iihr.res.in/international-conference-plant-protection-horticulture-icpph-2024-advances-and-challenges

Key Responsibilities Collaborate with Leading Scientists and Researchers to Secure Essential Funding The primary responsibility of the Grant Writing Specialist is to craft compelling grant proposals aimed at securing funding from diverse sources. This involves close collaboration with Umami Bioworks' world-class team of scientists and researchers, ensuring that proposals accurately reflect the company's innovative bioengineering projects and their potential global impact. Qualifications and Expertise Required The Ideal Candidate for the Grant Writing Specialist Role Successful candidates will possess exceptional communication and writing skills, with a proven track record in securing significant grants. Familiarity with the funding landscape and experience in navigating the specific requirements of various grant agencies is critical for success in this role. Candidates must be able to articulate complex bioengineering concepts in a clear and persuasive manner. Why Choose Umami Bioworks? Be Part of a Mission-Driven Company Pioneering the Future of Bioengineering Umami Bioworks offers more than just a job; it provides a platform to work on groundbreaking projects with real-world implications. As a **Grant Writing Specialist**, professionals will have the chance to contribute to a team that is actively shaping the future of bioengineering, with innovations that could impact global health, sustainability, and food production. How to Apply? Visit: https://careers.umamibioworks.com/jobs/4795976-grant-writing-specialist

Bioinformatics Analyst Position Institution: Albert Einstein College of Medicine Department: Pediatrics Job ID: 2024-16252 Location: Einstein/Resnick - Bronx Position Type: Regular Full-Time Salary Range: $58,500 - $65,000 per year Position Overview The Albert Einstein College of Medicine is seeking a motivated and experienced Bioinformatics Analyst to join Dr. Robert Burk's research group. This role is integral to supporting ongoing research projects focused on two primary areas: the human microbiome (gut, oral, and cervicovaginal) and human papillomavirus related to cervix neoplasia. Key Responsibilities Perform demultiplexing and analysis of NGS data using barcoding primers for multiplex NGS runs Process and analyze high-throughput sequencing data reads, including amplicon sequencing, bisulfite sequencing, metagenomics, and viral integration Manage and organize bioinformatics sequencing data for the research group Handle large Fastq, BAM, and/or Fasta files for analyses Utilize existing software tools and modify R scripts for figure generation and epidemiological analyses Construct phylogenetic trees to support ongoing research projects Collaborate closely with the Principal Investigator and other lab members Qualifications Bachelor's degree with at least one year of experience in epidemiology, computational biology, or bioinformatics Proficiency in R or Python Experience in microbiome bioinformatic processing (preferred) Strong communication skills, both verbal and written Ability to present at weekly lab meetings using PowerPoint or other presentation programs Excellent interpersonal skills and ability to work collaboratively Strong problem-solving skills and ability to manage time effectively Innovative approach to applying technology to improve efficiency and solve research-related problems The ideal candidate will have a background in epidemiology, computer science, bioinformatics, or related disciplines, with practical demonstrated experience in processing next-generation sequencing (NGS) data. The successful applicant will demonstrate a willingness and eagerness to adapt to new approaches, recognizing the dynamic and constantly evolving nature of the bioinformatics field. This position offers an exciting opportunity to contribute to cutting-edge research in human microbiome and papillomavirus studies at a prestigious institution. The selected candidate will work in a collaborative environment, directly reporting to Dr. Robert D. Burk, the Principal Investigator, and interacting with other lab members generating NGS data.

What is Windows Subsystem for Linux (WSL Windows Subsystem for Linux (WSL) is a powerful tool that helps us install a desired Linux distribution (Ubuntu, OpenSUSE, Arch Linux, etc.), without the need for an overboard installation of a virtual machine, or dual boot machine Pre-requisites for the Installation of WSL You should be using Windows 10 version 2004 or higher (or Build 19041 or higher) or Windows 11 if you want to run the WSL command. One way to check is by opening the “RUN” window, and typing “ winver ”, as shown below. The window that appears shows the version of Windows that you have. You can also check the Windows version using the command prompt. Let’s look at the command a bit. Here, the “ findstr ” finds the strings that start with “ OS Name ” and “ OS Version ” Install WSL Next, you need to open the “ Turn Windows Features On or Off” On the window that you see above, you need to turn on “ Windows Subsystem for Linux ” and “ Virtual Machine Platform ” After you turn on both the features mentioned above, the system will apply the changes and you will have to restart your machine. A restart can be avoided using the following commands to turn on “ Windows Subsystem for Linux ” and “ Virtual Machine Platform ” For Windows Subsystem for Linux , For Virtual Machine Platform , Once the supportive Windows version is in place, now with a single command we can install WSL. Open the command prompt or  Powershell  with administrative privileges, and enter the following command. wsl —install But wait! This will by default install Ubuntu . Specifically, you can install a Linux distribution of your choice. Before that, we can check the available Linux distribution online. So, by entering the following command, we will be able to see the all Linux distributions that we can install in WSL. We can install a specific Linux distribution using the following command. wsl —install —d After the successful installation is over, the CMD  looks as follows. Sometimes you may encounter an error as follows. Here the error message says the WSL2 requires an update to its  kernal  component. To update to WSL 2, you need to be running Windows 10 or Windows 11. And following are the individual requirements for x64-based PC and Arm64-based PC. For x64 systems:  Version 1903  or later, with  Build 18362.1049  or later. For ARM64 systems:  Version 2004  or later, with  Build 19041  or later To check if it is an x64 or ARM64 system, use the following command. You can check the version/ build using the method mentioned in the initial segment of this article. Download the Linux Kernal Update Package Now, you can download the Linux kernel update package. If you want to download the update package from the Microsoft Store, use one of the following commands. You can use either wsl.exe --install  or  wsl.exe --update Or, depending on whether you are using the x64-based or ARM64-based PC, you can manually download and install the update package. For x64-based PC, https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_x64.msi For ARM64-based PC, https://wslstorestorage.blob.core.windows.net/wslblob/wsl_update_arm64.msi Set WSL2 as default Now, WSL2 can be set as our default version using the following command. Finally, we have the terminal window Use the Ubuntu terminal as a new tab of the Windows terminal You can also have the Linux terminal as a new tab of the Windows Terminal. For this, when you open the Windows terminal, you may notice the downward arrow. Click it and choose the terminal window of your choice. Here, it is the Ubuntu terminal.