FSCS – NOAA Teacher at Sea Blog

September 20, 2024September 20, 2024

Sam Garson: Alexa, What Fish Is This? September 20, 2024

NOAA Teacher at Sea

Sam Garson

Aboard NOAA Ship Henry B. Bigelow

September 6^th – September 25^th, 2024

Mission: 2024 Fall Bottom Trawl Survey

Geographic Area of Cruise: Northeast Atlantic Ocean

Date: September 20th, 2025

Weather Data:

Latitude: 35°31’43.1″N

Longitude: 75°16’18.3″W
Wind Speed: N 14.68 kt
Air Temperature: 22.9°C (73°F)

As a participant in NOAA’s Teacher at Sea program, I’ve had the incredible opportunity to see first-hand the innovative tools scientists use to study marine life. One such tool that has become indispensable is the Fisheries Scientific Computing System (FSCS), a specialized software developed to help scientists efficiently process the specimens brought up in trawl nets during research surveys. In this blog, I’ll take a closer look at how the FSCS software guides scientists through the complex task of collecting, analyzing, and recording biological data from the sea’s many inhabitants.

photo of a computer screen displaying the trawl monitoring software. we can see a graph of trawl depth over time. there are other readouts that are not legible. — Trawl Monitoring Software lets the Watch Leaders see if the parameters for a successful trawl were met.
Photo Credit: Sam Garson

What is FSCS?
The Fisheries Scientific Computing System (FSCS) is a powerful, custom-built software that NOAA scientists use to manage the massive amount of data gathered during trawl surveys. Every time a trawl net is brought aboard, scientists are faced with a diverse haul of marine specimens that need to be sorted, identified, measured, and cataloged. FSCS streamlines this entire process, ensuring that data are collected accurately and consistently across multiple surveys and locations.

photo of the computer screen at the cutting station that displays the FSCS program. Currently, the screen shows the list of names of possible science team members, and to the right, the assignments at this station: Cutter - Sabrina Dahl, Recorder - Sam Garson. at the base of the screen is a label that reads DO NOT SPRAY. — FSCS begins with the pair of scientists logging in with their roles of cutter or recorder. Photo Credit: Sam Garson

The FSCS software is designed specifically for the high-paced environment aboard research vessels, where time is of the essence. There are times during a busy string of trawl operations that a net’s worth of samples will barely be complete before the next net is already onboard ready to be dumped into the checker. It operates as a centralized platform, allowing scientists to record and track a variety of biological data, including species identification, lengths, weights, and even environmental conditions like water temperature and depth. By digitizing the data collection process, FSCS not only improves accuracy but also allows the information to be instantly accessible for analysis.

The Trawl Processing Workflow with FSCS
Once a trawl is hauled aboard, the real work begins. First, the catch is emptied into a sorting table called “the checker” where the catch is fed in manageable amounts onto the first conveyor belt and brought up into the sorting table. In the past, this sorting process involved manually recording data on paper, but FSCS has helped this step by providing real-time data entry directly into the system via rugged, waterproof touchscreens and computers.

Once the catch has moved down the sorting table it is processed by the Watch Leader into the system and then fed down the last conveyor belt to the 3 cutting stations. The Watch Leader is responsible for:

Species ID: Using guides and reference materials, scientists identify each species brought up in the trawl. This is important because in the paper log days, each container would be re-identified by the cutting team, and mistakes could be made with look-alike species. The system now removes this source of error.

a stack of three smaller screens, some with keypads, showing length and weight readings — Integrated scales and length measuring allow the team to move quickly and efficiently. Photo Credit: Sam Garson

From there, the specimens are processed one by one. For each fish or invertebrate species, scientists enter:

Length and Weight: FSCS is connected to precision scales and measuring boards, allowing data to be automatically uploaded into the system.
Sex and Maturity: For certain species, scientists may record sex and reproductive status to assess population dynamics.
Stomach Contents: For certain species the stomach volume and contents are examined and identified
Freeze Sample: Based on the research needs of scientists ashore and programs supported by the trawl, certain species are collected, bagged and frozen for further processing back ashore.

FSCS’s intuitive interface helps guide scientists through this complex process, ensuring no key steps are missed. It also automatically flags any anomalies, such as unusually large or small specimens, prompting scientists to re-check measurements for accuracy.

photo of a computer screen display showing a list of closed drop-down menus titled "Organism 133," "Organism 134," etc to "Organism 148" — Sometimes there is a LOT of processing to do! Photo Credit: Sam Garson

Why FSCS is Important for Marine Research
The FSCS software plays a critical role in ensuring the consistency and accuracy of data collection across NOAA’s bottom trawl surveys. Since the same software is used across different vessels and surveys, it standardizes the way data are collected, which is essential when comparing long-term trends in fish populations and marine ecosystems.

Furthermore, FSCS dramatically reduces the risk of human error, which can be a challenge when processing hundreds or even thousands of specimens in a single day. By integrating measurement devices directly into the software, FSCS ensures that all data are automatically logged without the need for manual entry, reducing errors and speeding up the overall workflow.

This efficiency is particularly important for scientists working in the field, where time is often limited. With FSCS, scientists can process specimens more quickly and move on to analyzing the data, which helps them make faster, more informed decisions about the health of fish populations and ecosystems. The software also allows for real-time data transfer, meaning that the data collected can be immediately uploaded to NOAA’s central databases for use in managing fisheries and conservation efforts.

FSCS and Data-Driven Decisions
The data collected through FSCS are vital for the sustainable management of marine resources. By providing real-time, high-quality data on fish populations, FSCS helps inform decisions about fishing quotas, endangered species protections, and ecosystem conservation measures. The software ensures that scientists have access to accurate, up-to-date information, which is crucial for making data-driven decisions that can have long-lasting impacts on the health of our oceans.

NOAA uses the data collected through FSCS to assess the status of important commercial fish species like cod, haddock, and flounder. These assessments along with commercial catch data form the basis for setting annual catch limits and developing regulations to prevent overfishing and ensure that fish populations remain healthy for future generations.

Personal Log

During my time aboard the NOAA Ship Henry Bigelow, I have had the opportunity to observe the close collaboration between scientists and crew members during trawling operations. Each person, from the captain navigating the ship to the scientists analyzing the catch, contributes their expertise to ensure the success of each trawl. It’s evident that communication and coordination are at the core of every operation, with everyone knowing their role and adapting as needed to changing conditions.

What stands out most is how the team handles the demanding work involved in trawling. The deck crew efficiently deploys and retrieves the nets, often under challenging conditions, while the scientists are quick to sort, measure, and record data on various species. The entire process is a well-practiced routine, yet there is constant attention to detail and safety. This level of cooperation is not just about completing the task but about ensuring that the data collected is reliable and valuable for ongoing research.

Watching the crew and scientists work together has given me a deeper understanding of the complexities involved in marine research. It’s not just the technical skills that matter but the ability to work as a cohesive team, problem-solve on the spot, and maintain a shared focus on the mission. This experience has been an eye-opening look at the dedication and collaboration required to conduct scientific research at sea.

What coding language does a fish use?

Sea++

Did You Know?

A fun fact about sea robins is that they have “legs” and “wings”! While they don’t actually have legs, sea robins possess spiny, modified pectoral fins that look and act like little legs, allowing them to “walk” along the ocean floor. These fins are used to feel for prey like crabs, shrimp, and small fish. Additionally, their large, wing-like pectoral fins can be spread out like a fan, making them look like they’re flying underwater—adding to their unique and quirky appearance!

highly detailed scientific photo of a preserved specimen of a sea robin against a black background — Northern Sea Robin Photo Credit: Harvard Museum of Comparative Zoology

April 30, 2015August 21, 2021

Emily Whalen: Trawling in Cape Cod Bay, April 29, 2015

NOAA Teacher at Sea
Emily Whalen
Aboard NOAA Ship Henry B. Bigelow
April 27 – May 10, 2015

Mission: Spring Bottom Trawl Survey, Leg IV
Geographical Area of Cruise: Gulf of Maine
Date: April 29, 2015

Weather Data:
GPS location: 42^○51.770’N, 070^○43.695’W
Sky condition: Cloudy
Wind: 10 kts NNW
Wave height: 1-2 feet
Water temperature: 6.2^○C
Air temperature: 8.1^○C

Science and Technology Log:

On board the Henry B. Bigelow we are working to complete the fourth and final leg of the spring bottom trawl survey. Since 1948, NOAA has sent ships along the east coast from Cape Hatteras to the Scotian Shelf to catch, identify, measure and collect the fish and invertebrates from the sea floor. Scientists and fishermen use this data to assess the health of the ocean and make management decisions about fish stocks.

What do you recognize on this chart? Do you know where Derry, NH is on the map? — This is the area that we will be trawling. Each blue circle represents one of the sites that we will sample. We are covering a LOT of ground! Image courtesy of NOAA.

Today I am going to give you a rundown of the small role that I play in this process. I am on the noon to midnight watch with a crew of six other scientists, which means that we are responsible for processing everything caught in the giant trawl net on board during those hours. During the first three legs of the survey, the Bigelow has sampled over 300 sites. We are working to finish the survey by completing the remaining sites, which are scattered throughout Cape Cod Bay and the Gulf of Maine. The data collected on this trip will be added to data from similar trips that NOAA has taken each spring for almost 60 years. These huge sets of data allow scientists to track species that are dwindling, recovering, thriving or shifting habitats.

At each sampling station, the ship first drops a man-sized piece of equipment called a CTD to the sea floor. The CTD measures conductivity, temperature and depth, hence its name. Using the conductivity measurement, the CTD software also calculates salinity, which is the amount of dissolved salt in the water. It also has light sensors that are used to measure how much light is penetrating through the water.

While the CTD is in the water, the deck crew prepares the trawl net and streams it from the back of the ship. The net is towed by a set of hydraulic winches that are controlled by a sophisticated autotrawl system. The system senses the tension on each trawl warp and will pay out or reel in cable to ensure that the net is fishing properly.

Once deployed, the net sinks to the bottom and the ship tows it for twenty minutes, which is a little more than one nautical mile. The mouth of the net is rectangular so that it can open up wide and catch the most fish. The bottom edge of the mouth has something called a rockhopper sweep on it, which is made of a series of heavy disks that roll along the rocky bottom instead of getting hung up or tangled. The top edge of the net has floats along it to hold it wide open. There are sensors positioned throughout the net that send data back to the ship about the shape of the net’s mouth, the water temperature on the bottom, the amount of contact with the bottom, the speed of water through the net and the direction that the water is flowing through the net. It is important that each tow is standardized like this so that the fish populations in the sample areas aren’t misrepresented by the catch. For example, if the net was twisted or didn’t open properly, the catch might be very small, even in an area that is teaming with fish.

Do you think this is what trawl nets looked like in 1948? — This is what the net looks like when it is coming back on board. The deck hands are guiding the trawl warps onto the big black spools. The whole process is powered by two hydraulic winches.

After twenty minutes, the net is hauled back onto the boat using heavy-duty winches. The science crew changes into brightly colored foul weather gear and heads to the wet lab, where we wait to see what we’ve caught in the net. The watch chief turns the music up and everyone goes to their station along a conveyor belt the transports the fish from outside on the deck to inside the lab. We sort the catch by species into baskets and buckets, working at a slow, comfortable pace when the catch is small, or at a rapid fire, breakneck speed when the catch is large.

If you guessed 'sponges', then you are correct! — This is the conveyor belt that transports the catch from the deck into the wetlab. The crew works to sort things into buckets. Do you know what these chunky yellow blobs that we caught this time are?

After that, the species and weight of each container is recorded into the Fisheries Scientific Computing System (FSCS), which is an amazing software system that allows our team of seven people to collect an enormous amount of data very quickly. Then we work in teams of two to process each fish at work stations using a barcode scanner, magnetic lengthing board, digital scale, fillet knives, tweezers, two touch screen monitors, a freshwater hose, scannable stickers, envelopes, baggies, jars and finally a conveyor belt that leads to a chute that returns the catch back to the ocean. To picture what this looks like, imagine a grocery store checkout line crossed with an arcade crossed with a water park crossed with an operating room. Add in some music playing from an ipod and it’s a pretty raucous scene!

The data that we collect for each fish varies. At a bare minimum, we will measure the length of the fish, which is electronically transmitted into FSCS. For some fish, we also record the weight, sex and stage of maturity. This also often includes taking tissue samples and packaging them up so that they can be studied back at the lab. Fortunately, for each fish, the FSCS screen automatically prompts us about which measurements need to be taken and samples need to be kept. For some fish, we cut out and label a small piece of gonad or some scales. We collect the otoliths, or ear bones from many fish.

It does not look this neat and tidy when we are working! — These are the work stations in the wet lab. The cutters stand on the left processing the fish, and the recorders stand on the right.These bones can be used to determine the age of each fish because they are made of rings of calcium carbonate that accumulate over time.

Most of the samples will got back to the Northeast Fisheries Science Center where they will be processed by NOAA scientists. Some of them will go to other scientists from universities and other labs who have requested special sampling from the Bigelow. It’s like we are working on a dozen different research projects all at once!

Something to Think About:

Below are two pictures that I took from the flying bridge as we departed from the Coast Guard Station in Boston. They were taken just moments apart from each other. Why do you think that the area in the first picture has been built up with beautiful skyscrapers while the area in the second picture is filled with shipping containers and industry? Which area do you think is more important to the city? Post your thoughts in the comment section below.

Rows of shipping containers. What do you think is inside them?

Downtown Boston. Just a mile from the shipping containers. Why do you think this area is so different from the previous picture?

Personal Log

Believe it or not, I actually feel very relaxed on board the Bigelow! The food is excellent, my stateroom is comfortable and all I have to do is follow the instructions of the crew and the FSCS. The internet is fast enough to occasionally check my email, but not fast enough to stream music or obsessively read articles I find on Twitter. The gentle rocking of the boat is relaxing, and there is a constant supply of coffee and yogurt. I have already read one whole book (Paper Towns by John Greene) and later tonight I will go to the onboard library and choose another. That said, I do miss my family and my dog and I’m sure that in a few days I will start to miss my students too!

If the description above doesn’t make you want to consider volunteering on a NOAA cruise, maybe the radical outfits will. On the left, you can see me trying on my Mustang Suit, which is designed to keep me safe in the unlikely event that the ship sinks. On the right, you can see me in my stylish yellow foul weather pants. They look even better when they are covered in sparkling fish scales!

Seriously, they keep me totally dry! — Banana Yellow Pants: SO 2015! Photo taken by fellow volunteer Megan Plourde.

Seriously, do I look awesome, or what? — This is a Mustang Suit. If you owned one of these, where would you most like to wear it? Photo taken by IT Specialist Heidi Marotta.

That’s it for now! What topics would you like to hear more about? If you post your questions in the comment section below, I will try to answer them in my next blog post.

September 25, 2012August 11, 2021

Kaitlin Baird: Did You Know? September 25, 2012

NOAA Teacher at Sea
Kaitlin Baird
Aboard NOAA Ship Henry B. Bigelow
September 4 – 20, 2012

Mission: Autumn Bottom Trawl Survey with NOAA’s Northeast Fisheries Science Center
Geographical Area: Back in port! Newport Rhode Island
Date: September 21st
.

Location Data:
Latitude: 41’53.04
Longitude: 71’31.77

Weather Data:
Air Temperature: 13.8 (approx.57°F)
Wind Speed: 10.01 kts
Wind Direction: North
Surface Water Temperature: 19.51 °C (approx. 67°F)
Weather conditions: overcast

Science and Technology Log:

I thought I would end my trip on the Henry B. Bigelow with some fun facts!

Did you know?

The Fisheries Scientific Computer System (FSCS) is able to prompt the data recorders with all actions needing to be performed for a particular species. It is coded with unique barcodes for every sample taken. Back in the laboratory all scientists receiving samples can receive all the information taken about the given organism by scanning this unique barcode!

barcoding for species caught on cruise for further analysis — Barcoding for species caught on cruise for further analysis

Did you know?
Science crew operating on the back deck are required to wear an Overboard Recovery Communications Apparatus (ORCA). This system if it is activated sends a signal by way of radio frequency to a receiver on the ship’s bridge. This system responds immediately to the ship receiver and has a direction finder to help locate the man overboard.

Me getting ready to head to the back deck with my positioning system around my neck — Me getting ready to head to the back deck with my ORCA around my neck

Personal Log:

It would take me hours to go through all of the amazing creatures we caught and surveyed on this trip, so I thought I would write some fast facts about some of my favorites! Enjoy!

Did you know?

The male spoon arm octopus has a modified arm that passes spermatophores into the oviducts of the female. Pretty neat stuff!

Did you know?
Stargazers, like this one, have an electric organ and are one of few marine bony fish species that are able to produce electricity. This is known as Bioelectrogenesis. They also hide beneath the sand with just their eyes sticking out and ambush their prey!

Did you know?
This fish, the Atlantic midshipman, has bioluminescent bacteria that inhabit these jewel–like photophores that emit light! It also interestingly enough uses this function in fairly shallow waters!

midshipman photophores — Midshipman photophores

Did you know?
Sea spiders like this one have no respiratory organs. Since they are so small gasses diffuse in and out of their bodies, how cool is that!

Did you know?
The flaming box crab, Calappa flammea, uses its scissor-like claws that act as a can opener. It has a special modified appendage to open hermit crabs like a can opener!

Did you know?
A female Atlantic angel shark like this one can have up to 13 pups!

Did you know?
Seahorses suck up their food through their long snout, and like the flounders I talked about at the beginning of the cruise, their eyes also move independently of each other!!

Did you know?
Horseshoe crabs, like this one, have blue blood. Unlike the blood of mammals, they don’t have hemoglobin to carry oxygen, instead they have henocyanin. Because the henocyanin has copper in it, their blood is blue!

Last but NOT least, Did you know?
According to the Guiness Book of World Records the American Lobster has been known to reach lengths over 3 ft (0.91 m) and weigh as much as 44 lb (20 kg) or more. This makes it the heaviest marine crustacean in the world! This one was pretty large!!

A big farewell to everyone on the Henry B. Bigelow! Thanks so much, i had a great time and learned a lot! Thanks for reading!

September 14, 2012August 11, 2021

Kaitlin Baird: Some Essential Tools! September 14, 2012

NOAA Teacher at Sea
Kaitlin Baird
Aboard NOAA Ship Henry B. Bigelow
September 4 – 20, 2012

Mission: Autumn Bottom Trawl Survey with NOAA’s North East Fisheries Science Center
Geographical Area: Off the Coast of Cape Hatteras, North Carolina
Date: September 14th
.

Location Data:
Latitude: 35′ 10.67
Longitude: 75’33.60

Weather Data:
Air Temperature: 23.40 (approx.74 °F)
Wind Speed: 2.17 kts
Wind Direction: Southwest
Surface Water Temperature:2 7.61 °C (approx. 82°F)
Weather conditions: Sunny and fair

Science and Technology Log

One of the things I was curious about was the deployment of these large instruments and the technology that supports it. One of the keys to the deployment of things like the BONGO nets, Continuous Depth Recorders (CTD’s) and the trawl net itself are winches. A winch spools the wire cable that is hooked to all of the instruments and allows them to move up, down and out into the water column. With some of the instruments, like the BONGO’S and CTD casts, a retractable A-Frame is used to lower the cable from the winch. You can see the A-Frame on the right and the winch on the left in the photo below. This winch in particular controls the deployment of the net and connects to two winches on the stern that roll out the net to open up the mouth. The wire is constantly monitored from the bridge on the screen below and is automatically adjusted to maintain equal tension on both sides.

Winch for fishing nets, Tension monitor on winches from the bridge and A-frame — Winch for fishing nets, Tension screen for winches from the bridge and retractable A-frame

Once the net is run out with the aid of the winches, it is constantly monitored for its shape during the tow with a number of different censors attached to the net. There is an autotrawl system that sets the depth of the trawl and the tension of the wires. A Global Positioning System (GPS) plots the position of the net for each trawl so that it can be associated with all organisms caught in the tow. At the end of the tow the winches reel back the cable and a crane brings the net with the catch over to the “checker” where the net is unloaded!

Monitoring the position and shape of the trawl in the water

Personal Log:

The fun part begins when the net opens and all the animals enter the checker. When all of the catch goes into the checker the scientists take a look at the catch, and remove anything too large to go up the conveyor belt. If a fish dominates the catch it will “run”. This means, as it goes down the conveyor belt it won’t be taken off and it will be weighed by the basketful and then a subsample will be taken for further analysis.

The fish are all divided up by species and electronically coded in the FSCS system to be measured. After they are measured, the system will prompt for further analysis for that particular species. If extra sampling of the fish is required, it is labeled with a printed sticker for the species with a unique barcode that can be scanned to retrieve its record in the database.

tag for the organisms to designate its ID and what is to be done with it — Tag for the organisms to designate its ID and what is to be done with it

I thought I’d share some photos with you of some of the unique things we have seen so far fishing today. We are off the coast of Carolina and finishing up our Southern stations today into early morning!

Catch of the day! Thanks for reading!

Atlantic Sharpnose Shark caught off of Carolina coast

September 7, 2012August 11, 2021

Kaitlin Baird: All Ashore Who Are Going Ashore, September 6, 2012

NOAA Teacher at Sea
Kaitlin Baird
Aboard NOAA Ship Henry B. Bigelow
September 4 – 20, 2012

Mission: Autumn Bottom Trawl Survey with NOAA’s North East Fisheries Science Center
Geographical Area: Atlantic Ocean steaming to south New Jersey coast
Date: September 6, 2012

Location Data:
Latitude: 41 ° 18.70’ N
Longitude: 71 ° 42.11’ W

Weather Data:
Air Temperature: 20.5°C (approx. 69°F)
Wind Speed: 4.97 kts
Wind Direction: from N
Surface Water Temperature: 22.2 °C (approx. 72°F)
Weather conditions: Sunny and fair

Science and Technology Log

The purpose of our mission aboard the Henry B. Bigelow is the 1st leg of groundfish surveys from Cape May all the way down to Cape Hatteras with the Northeast Fisheries Science Center. The scientists aboard the ship are interested in both the size and frequency of fish at different targeted geographic locations. We will be sampling using a trawl net at about 130 different stations along the way, some inshore and some offshore. We will be using a piece of technology called the Fisheries Scientific Computer System (FSCS). This system will allow us to accurately take baskets of different species of fish and code them for their lengths into a large database. This will give us a snapshot of fisheries stocks in the Northeast Atlantic by taking a subsample. The computer system also allows us to see if any other things need to be done with the fish once they are measured. Tasks like otolith (I’ll tell you about these later!) and gonad removal, fin clips or whole organisms sampling may also be done. The computer system will allow us to label each of these requests and assign it a code for scientists requesting samples from this cruise. Additionally, there are scales along with the system for recording necessary weights. We will be sorting fish first by species, and then running them all through the coded FSCS which you can see in the photo below.

Measuring board for fish — Board for magnetically measuring fish

We are currently on full steam to get our first tow in early tomorrow morning. You can track our ship using NOAA’s ship tracker system. Here we are positioned currently passing Block Island.

Ship Tracker with Current Location — NOAA Ship Tracker

Can’t wait to tell you more about the FSCS system when we start using it tomorrow!!

Personal Log

We have just pushed off the dock at 0900 and are headed South to start our first trawl tomorrow morning. Everyone is getting used to the ship and some swells with a few storms in the Atlantic. I am really excited to get to see what comes up in our first tow. I have been assigned to the day watch which means that my shift runs from Noon-Midnight. The two other ladies that share our room will be on the night watch, so there will be a changing of the guard and some fresh legs and recorders.

Darcy and Caitlin two other volunteers learning the ropes

All ready to go — Helly Hansen gear to keep us all dry.

I am looking forward to bringing you some cool fish photos soon! Hello to everyone back in Bermuda! Stay safe..

Bye for now!!