I am a Senior Product Manager at DNASTAR – my job is to manage the road map for our software products and communicate these ideas to others in the company. AMA about molecular biology and genomics software tools.

As an aspiring Senior Product Manager, I'm more curious about your day to day and what it is you consider your role and major deliverables? What skills should I focus on if I want to be you?

FYI, I am a software engineer, in a sr developer role with a fair amount of management responsibilities, especially mentorship of new hires.

In a software company, the "Product Manager" role sits at the intersection of Development, Marketing and Sales and has to act as a conduit of information between these teams and to the company stakeholders. In addition, the PM must have an overall product vision and maintain a product roadmap. The PM in smaller companies may also help with QA, project management and supporting Sales.

At DNASTAR, we use a modified scrum style development and the JIRA platform to manage different projects. We use Slack to communicate between different subgroups within the company. My daily tasks involve monitoring development progress and making sure that what gets developed is what the customer wants and meets the criteria for the satisying that customer need. I also have several lines of communication with the Sales team who pass along all customer feedback that I process and place into the appropriate JIRA story. I may also assist with customer technical support as part of this feedback (again, small company). I also work with Marketing to review materials and in some cases, create some of the materials they need to promote our products. Marketing also collects user feedback that is incorporated into development decisions.

So, I think the main skills are really a willingness to be very transparent about the process, so that everyone sees the benefit in participation in reaching a common goal - a better product.

Thanks, that was a really helpful answer and I appreciate your taking time to post it!

You are welcome!

Do you have product owners as well within your structure or anything like one?

Yes, we use the concept of product owners as well. We're a small company, so product owners have dual titles. Product ownership is essential so that there is a single person that has responsibility for a product, even when it is not part of an active development cycle. Without POs, products can fall through the cracks.

What is the intersection of your role and theirs?

It's a large intersection. I am the product owner of several of our most used applications. I think this is common in small companies where individuals need to fill multiple roles. Our scrum teams typically consist of Product owner, Project manager, QA lead, Scientific lead, developers and (sometimes) a scrum master. For some of these teams, I function as the product owner, for other teams we may have a scientific lead that functions in that capacity.

But why male models?

Sorry, I don't understand your question.

I have been a DNASTAR user since the 90's - recently upgraded my os to Catalina - and thus the new "Pro" and "Ultra" software - and it is NOT working well for me - crashing and poor performance. Are there any fixes on the horizon?

Sorry to hear that you are having issues with the latest software. The Mac platform has been especially challenging the past year with Catalina and now Big Sur, both of whom presented significant changes requiring a lot of updating on our end. DNASTAR is releasing a patch this week that addresses Big Sur compatibility and fixes many new and remaining ssues with Catalina. Also, with respect to Sanger data assembly and analysis, much of the functionality in SeqMan Pro has now been migrated to SeqMan Ultra.

Hi Matt

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I enjoyed your webinars and thanks for the opportunity to ask. I would like to have some help on genomics. I have VCF results from a panel and now I have managed to annotate and see the SNPs on Array star. What is the next steps in order to see if there is a special mutation on my genes of interest? Because each gene has a lot of SNPs, how to choose which I have to go on ? Do I have to compare all the samples for each SNPs or I can select somehow the most important ? I need kind of workflow after annotation

That is the big challenge with variant analysis. Even with initial filtering there still may a lot more SNP variants remaining than is practical to analyze. One strategy is to compare samples and identify variants that are common or unique to the sample groups. Also, for some model organisms, DNASTAR provides Genome Template Packages that can be used at assembly time (or VCF file import time) that provide additional annotation that can be used to identify important variants. For example, GERP scores that assign weight (evolutionary conservation) to variations and can be used to identify variants that occur at more impactful locations. If you are working with human data, we also offer the Variant Annotation Database that provides a huge amount of additional variant annotation from dbNFSP, MasterMind (Genomenon), 1000 Genomes allele and genotype frequencies. We have a recently updated VAD page that explains these databases in more detail <https://www.dnastar.com/variant-annotation-database/>

What tools do you use for your roadmap, and in which form do you have it? Is it just a presentation? Or a gantt chart? Or a spreadsheet? There are quite a few specialized apps like aha, shipit, prodpad, and many others, each doing it its own way. Or you have a completely different one fine-tuned for genomics (like some hardware companies have)?

The first tool I used was a big whiteboard. I used Venn diagrams to illustrate where our products currently were and where I wanted them to be. I moved these ideas to a real roadmap ProductPlan. ProductPlan is very easy to use and gets the big ideas across on a timeline. The details of each component of the Roadmap are then recorded in JIRA and we use versions in the backlog to organize ideas for future development. It's all fluid in the backlog, however, and items get re-prioritized on a regular basis as new feedback comes in.

Oh wow, never thought Venn diagrams could be used for that. Thanks for the explanation. Also curious to know why did you decide to work as a PM instead of continuing research or working in a lab? Don't you miss that?

I went from lab work to a Sales position at DNASTAR back in 2004. I became involved with product development almost immediately, but only as a part time gig. It wasn't until almost 10 years later that I fully transitioned to PM.

No, I don't miss working in a lab at all. Research probably moved a little too slowly for my tastes. Also, as a Sales rep, I helped customers with many projects that were a lot more interesting than the stuff I was working on. I probably can't mention them by name, but we have customers all over the world working on really cool stuff and that was really fun learning about their research and helping them when asked.

Hey there! As a Madison resident and software developer, I'm surprised I haven't heard of DNASTAR. How large is your software dev staff? Your site mentions proficiency in Java and C++ - what percentage of your codebase would you say is in each language? Are any of your applications available as webapps? If not, are you planning on moving any of them to the web?

Well, we are tucked away up in the Hoyt park neighborhood, so even our delivery guys have a hard time finding us! We have about 40 employees, with about half of those actual software engineers. Our newest software is written mostly in Java, with some C++ as well. We are not currently planning on developing webapps in the near future. Our business in mostly locally installed software that accessing the Cloud when needed.

Hi Matt, How long do you think before the entire process from raw reads to variant interpretation is entirely automated in the biomedical field?

It is certainly moving in that direction and small assays or panel can already be fully automated when specific variants are already known. However, variant interpretation is another thing. A typical human exome assembly with yield 10-15K variants and even after several layers of filtering, you are still left with dozens if not hundreds of variants that are potentially interesting. I think this interpreting even this filtered subset of variants will require knowledgeable human intervention, at least for the next few years.

How would one transition into the IT industry and possibly make their way up to a position of your caliber? I don't have any IT experience nor do I have a degree in anything related to science, CIS, computer science etc. I'm just desperate to do something new and don't know who to ask or speak to. For reference, I live in San Antonio so the job market is there and hiring despite what's happening in the world but I just don't know where to start.

I think everyone has their own unique career path, and mine was no different. In the mid-1990s I was working in a QA food products lab and was getting bored with it so I took a couple molecular biology classes in the evenings. A year later, I started grad school so I could learn as much as possible about molecular biology and really enjoyed developing new lab techniques and running experiments (not so much with writing papers and grants!). It was in grad school that I really learned how to use computers and DNA sequence analysis software and my career path took this direction. So, my advice is to just get your feet wet with IT/Bioinformatics. Take a class, see how you like it. Get some experience and find an internship where you can learn on the job and then grow into the higher level position that you can settle in to.

I appreciate the time you took to write back to me. Thank you for your input.

You are very welcome!

Sort of a general question from a layman but, do you have any insights on the progress being made confidently predicicting epigenetic expression?

I think real time single molecule sequencing (PacBio and Nanopore) provides a means to directly detect nucleotide modifications and is a significant improvement over previous methods for epigenetic analysis. I do not have much personal experience here, but the DNASTAR development team is focused on supporting long read analysis tools and this is an area where latest generation of sequencing provides many advantages.

Is the company Publicly traded? If it was,would you invest? Why,why not?

No, DNASTAR is a privately owned company. I would invest in any bioinformatics software company that has been in business for 30+ years, continuously works to improve their products, and has a large and loyal customer base.

If you could, I'd love for you to describe the tools and practices you use as part of being a product manager? In particular I'm interested in the chain between gathering input from the business and clients all the way to defining, tracking and delivering value via developers etc.

For reference I'm a software consultant comfortable leading teams and am recently finding myself in a more strategic advisory type role as some clients aren't great at defining what they want and the relative priority of their company outcomes etc. I reckon a legit product manager would be great at this.

I think I just answered most of your question. Not sure how to point you there, so I'll paste here and make a couple changes to answer your questions:

In a software company, the "Product Manager" role sits at the intersection of Development, Marketing and Sales and has to act as a conduit of information between these teams and to the company stakeholders. In addition, the PM must have an overall product vision and maintain a product roadmap. The PM in smaller companies may also help with QA, project management and supporting Sales.

At DNASTAR, we use a modified scrum style development and the JIRA platform to manage different projects. We use Slack to communicate between different subgroups within the company. My daily tasks involve monitoring development progress and making sure that what gets developed is what the customer wants and meets the criteria for the satisfying that customer need. I also have several lines of communication with the Sales team who pass along all customer feedback that I process and place into the appropriate JIRA story. It is very important that your PM can efficiently prioritize the customer feedback, manage the volume coming in using tools like JIRA, and that they really understand customer need - or you'll spend a lot of time developing things no one wants to buy!

I am doing a PhD now and I kind of got tricked into developing many experiments involving RNA sequencing and cloning. My interests are in computational biology (ML for bio) and I have been able to mostly work on this, but my advisor forces me to collect my own data without any collaboration (I don't have a bio background). While I have picked up the necessary skills, I'm worried that I'll be seen as having too much breadth and not enough depth. Would industry view someone like myself as valuable? I

I also developed several RNA protocols in our lab, without any previous experience: non-radioactive Northern blots, ribonuclease protection assays, whole tissue RNA in situ hybridizations, even some RNAi on living tissues. While I also probably wasted a lot of time re-inventing the wheel, the experience of developing these techniques on my gave me a deeper understanding than I would have gotten just using an off-the-shelf kit. So, "yes", what you are learning in your lab is valuable to folks in industry, because you have a deeper understanding, though trial and error, of how molecular biology works.

How often do you receive calls from people trying to purchase dynastar alpine skiis?

Can't say we have. But some people pronounce "DNASTAR" as "DYNASTAR".

I hope to become a PM sometimes in the future. I am just graduating with bachelors, any tips? I will most likely start my career (entry level) as a business analyst and not software developer, since I don't enjoy coding on my freetime.

I think the key is for you to fully understand what the customers' needs are. One way to do this is to start in a Sales position where you'll quickly learn why customers either like or don't like your product. If Sales doesn't suit you, a Marketing position that does surveys or asks you to meet customers face to face, such as tradeshows, would provide you with a good place to start.

I work as a project manager in the biomedical industry. The software development lifecycle has been stressful here, especially in the last year. Management has...implied that they plan to move me up in management but recent reorgs have me questioning this.

How does your role as product manager compare to the PMs below you working directly through the SDLC? Would you say that your position is less stressful than theirs or a different kind of stress?

I am frequently wearing the hat of multiple positions outside of a project manager including product owner/manager, and I'm curious how it is in other roles in the same (or similar) industry.

DNASTAR is a small company, so probably not as many strata as your company. However, prior to my current role, we really did product management by committee with representatives from different silos in the company. I found that a lot more stressful because it was so much more inefficient - we'd spend too much time discussing smaller issues that really weren't that important to the customer. And as a low level manager, there really was no way to improve this process. Once you are in a position to change how your teams do things, you can really focus on the things that matter, reduce hours in meetings and improve transparency between internal "silos".

There has been increased scrutiny of PCR as a diagnostic tool due to anecdotal reports of false positive/negative results in COVID tests. What is your approach to discussing the limitations of molecular diagnostics with laypeople?

It can be a difficult discussion. Everything has an error rate at some level, even diagnostic tools that are considered highly accurate. PCR is certainly considered one of those highly accurate tools. I'd guess false positives are most likely cross-contamination by the folks doing the test. False negatives are likely due to at which point in the virus infection that the sample was collected. Hard to explain this to a layperson, however, and I think there is still a lot unknown about viral levels in the days following exposure and how that affects the test.

So, I don't think its' the PCR that is the issue, more our less than complete understanding of the virus.

What are your thoughts on investing in genomics sector as a whole? For example the ARKG ETF that invests in several dozens of companies working on genomics.

To me it seems like a no-brainer that these companies will grow over the next 5-10 years but that's from my layman's perspective.

I'm not sure I'm the right person to ask about this. I sold my Illumina stock before it tripled in value!

How much is my DNA (/Data) worth? and is there a movement among the science community to alert the population as to it's value so we can avoid having our DNA info sold like users had their internet browsing data sold?

I don't know that I can answer that. In general, I find it difficult to find human sequence data that can be used for QA testing or to develop specific analysis tools. So the community tends to use a lot of the same human data sets like the "Platinum" genomes that are used as reference genomes or sequences from non-human data sources. Human data sets are also locked down and require special permission from sources like the Short read archive, so there is some coordinated effort to protect human sourced data.

thanks! can you envision a scenario where Human Data has a market value? It sounds like you already have that issue, i.e. could I allow you to sequence my DNA for QA?

alsoCambridge Analytica made browsing data valuable by using it to determine personality types and media consuption predictions, I have to image there are DNA profiles that would yield similar prediction data?

do you see this as an issue?

I think most people would be pretty reluctant to provide their DNA for Marketing purposes, I know I would be.

What is your opinion on the types of tests you can buy to test your ancestry or origin?

I haven't used them myself and really have no idea if one is better than the other or how accurate they are. My family has pretty good traditional ancestry traced back to Europe. But I suppose if you don't have that knowledge, some genetic ancestry would be really interesting. They also probably don't have to be extremely accurate to give you the broader picture of where your ancestors came from.

I would like to know how much Neanderthal DNA I have, though. My wife would argue "most of it".

What's your biggest advice to other product managers, and for creating roadmaps?

I answered a similar question earlier today:

In a software company, the "Product Manager" role sits at the intersection of Development, Marketing and Sales and has to act as a conduit of information between these teams and to the company stakeholders. In addition, the PM must have an overall product vision and maintain a product roadmap. The PM in smaller companies may also help with QA, project management and supporting Sales.

At DNASTAR, we use a modified scrum style development and the JIRA platform to manage different projects. We use Slack to communicate between different subgroups within the company. My daily tasks involve monitoring development progress and making sure that what gets developed is what the customer wants and meets the criteria for the satisying that customer need. I also have several lines of communication with the Sales team who pass along all customer feedback that I process and place into the appropriate JIRA story. I may also assist with customer technical support as part of this feedback (again, small company). I also work with Marketing to review materials and in some cases, create some of the materials they need to promote our products. Marketing also collects user feedback that is incorporated into development decisions.

So, I think the main skills are really a willingness to be very transparent about the process, so that everyone sees the benefit in participation in reaching a common goal - a better product.

I do STR analysis of profile development and comparisons for legal ends. We use a mixture deconvolution software called ArmedXpert. The program is pretty outdated and a bit of a pain to use considering how it was created. Is there a program you could recommend if you are familiar with this type of work?

We offer tandem repeat detection in our GeneQuest module, though it is not specifically designed for STR profiling and sample comparison. I did a Google search and there appears to be some options, though I am not familiar with them. BTW, we will be retiring our GeneQuest module in the next year or so, I will create a JIRA story to add STR profiling to the replacement tool.

How do you manage your time, splitting strategic thinking and tactical thinking. How much of your week is spent with the devs, sales, alone just thinking?
Also, how much of your time is writing, speaking, thinking? It's a busy job!

That's highly variable for me. As we get closer to a software release, I spend a lot of time testing the new features, making sure that they meet the criteria from the users' perspective. I also comb through the JIRA backlog and make sure all issues are addressed for that release and all prioritize issues for the next release. This is also the time to create larger stories and epics for future releases and includes creating mockups and reviewing competing products and customer feedback. I take part in weekly "standup" planning meetings with each development team as well as Marketing, and am in constant Slack communication with Sales. So yes, very busy job!

On a scale from 1 to 10, with ten being the highest, what level is your fear of the "grey goo" scenario?

1

Do you use OKRs or a different method for tracking your goals for an upcoming period? Also how strict are you with your definition of ready and definition of done (if you use this too!).

We use a Roadmap and not OKRs as described by Marty Cagan in his product management book Inspired. That said, we use Roadmaps just for broad overviews of where we are going and what we have addressed over larger lengths of time. It's visual and easier for stakeholders that may not have intimate knowledge of the entire development effort. We do use OKRs with clear objectives defined - I'd call them "super-stories" in JIRA that we use for initial discussion, then split up into workable units. For some teams, we have very clear definitions of "ready" and "done". The "done" criteria is very important to limit feature creep and to time box efforts in certain areas.

Thanks Matt, I’ve just finished my first year as a product owner and still feel like I’m learning the ropes.

Any advice for how to manage stakeholders that have requirements that fundamentally will never get prioritised against other pieces of planned work due to them not being worth the dev time against other things on a roadmap?

Edit: also to add to this, do you factor in cost of delay when going through your planning cycles?

Yeah, that's a big challenge for product owners. I'm not sure I have a great answer for you other than taking the stakeholder's ideas and vetting it through the same process as the ideas that do get prioritized. Does this idea produce a product that customers want? Does the idea provide a competitive advantage? Have customers requested this functionality? Do Marketing surveys support this idea? You get the idea.

But always be prepared to defend your decision on a moments notice, not to prioritize these ideas and before you bury them in the backlog!

I can't see we factor in "cost of delay" in a quantifiable manner. Probably everything on our Roadmap has a cost of delay - some tracks more than others.

Hi Matt, I'm a PhD student working on my dissertation proposal where I'm looking at the programming habits of scientist programmers. Beyond yourself, do you have members of your development team with a background in molecular biology?

We do have some programmers with biology backgrounds, others learn a good amount of biology on the job. I think there are a lot of parallels between programming and sequence analysis, so these folks pick up the biology surprising quickly!

What are good undergraduate resources for someone looking to get started in these kinds of bioinformatics tools?

I used Pedro's Molecular Biology Tools back in the day. Now there are many, many different collections of open source tools that you have access to if you want to learn about them. If your lab (if you are in a lab) needs a set of tools, I'd recommend a commercial solution like DNASTAR, though. I just looked at Pedro's tools and it looks like a lot of them that I used for my research are now gone.

I recently moved from the bench to a scientific marketing company. My background is in molecular biology and bioinformatics. Any advice for a newbie like myself entering the strange field of marketing?

Marketing is a whole different beast. You may find that a lot of the marketing folks at your company do not have molecular biology or bioinformatics background. Those folks are scarce. So, you can use your background to help fine tune Marketing messages to make sure that they are on point biologically speaking.

What would you say would be the minimum budget for starting a genomics-centric software company?

That's a difficult one for me to answer. Over 30 years ago, DNASTAR started in the founders' basement without a lot of initial investment. If you can identify a niche that isn't currently well occupied, you could start with web apps without much initial investment. The key is to know where current users are having difficulty with the options that are already out there and then come up with a solution for them.

Are you guys hiring? 👀 Relevant bachelors degree

Check out our website for current position openings. We are always on the lookout for qualified individuals https://www.dnastar.com/about/careers/

Did you or others in similar roles to your own get a Scrum certification?

Yes, we have individuals with Scrum certification and they were instrumental in implementing our version of Scrum.

Which tool annoys you the most but is too political/costly to just replace?

I'm going to give a political answer on that one. Over the past year, we released SeqMan Ultra (Java based) to replace SeqMan Pro which was written on an old code base no longer support by the Mac OS. It was both costly and political to replace SeqMan Pro, but necessary to provide SeqMan functionality that works on all modern OS accomodates both long term and new users. DNASTAR still has a couple programs that will need to be replaced soon, it's just part of the normal software lifecycle.

And you’re going to have to intervene again soon now that Apple make their own silicon.

Thank you for your answer though. You didn’t need to be political on my behalf, I’m not a fan of political correctness.

Yes, Silicon will present similar challenges, but DNASTAR has a 30+ year of supporting the Mac platform and there are no plans to change that!

For someone not in the Life Science segment, how much do your solutions cost? I'm in the engineering segment and we use off the shelf software like AutoDesk suites, SolidWorks which can cost around $2,000USD per license per year.

Do you have customers who do biohacking as a hobby and use your software?

Our annual pricing is listed on our website and available via eCommerce. There are a range of prices, depending on what you need between $249 and $2399/yr. for an academic license.

Not sure what "biohacking" is? Sounds illegal.

I know you’ve touched on the day-to-day, but honing on one specific part which I think is pretty important: to what extent is a PM responsible for generating new ideas for products / features / tweaks?

And if it’s a combination of teams doing that, could you attribute approximate %s anecdotally to which teams are responsible for ~how much of that idea generation?

At DNASTAR, the PM is mostly responsible for features and incremental improvements. New product ideas is a group effort. DNASTAR has grant funded development projects that really push the envelope for new products and some of our stakeholders play a central role in innovation. So, for these projects my role is to turn these ideas into products that customers are willing to pay for.

What's the best path for a seasoned software engineer to get into bio space? Do you have to have biology degree as well or CS is enough?

We don't require a biology degree if a candidate has a high degree of proficiency. There just aren't enough developers with biology backgrounds, and if we limited our search in that way, we'd pass up some of our best engineers. We have plenty of folks, myself included that can teach enough of the biology to get the job done.

What percent of the Rat genome have you guys mapped to a GO Molecular Function?

I don't know the answer to that. Our customers can import GO annotations from the GO consortium (download .goa files), but I don't know how many of the rat genes have GO information associated with them.

Hi there,
-What du you think about Deepminds recent solution on the protein folding problem and how do you think will it affect the future of genomics and molecular biology?

-Is it worth to invest in genetic stocks?

I don't know a lot about the Deepminds solution, that may have been discussed in our previous AMA with Steve Darnell who leads our protein modeling team.

I don't think I want to guide anyone investments. Like I mentioned yesterday, I sold my Illumina stock before they tripled in value!

Hi Matt, nice to meet you!

What is your opinion about the prospect of machine learning/deep learning (ML/DL) in solving molecular biology problems?

I mean that recently, ML/DL gains some marvelous achievements such as AlphaFold. Do you think ML/DL is promising in molecular biology research?

We've had a few questions about machine learning and I'll admit, I'm not an expert here. Maybe this is a good topic for another AMA with someone that knows what they are talking about on this subject.

ML has been a frequent topic of conversation amongst our development team for a variety of challenges in assembly algorithms as well as protein modeling. The "Pros" are that ML can resolve very difficult problems, the "Cons" are that ML doesn't always scale very well, so time can be a limiting factor.

Can we terraform mars with crispr fungus Nd lichen?

Maybe.

Don't hate me for asking this, but what do you think your differences are with Benchling? I'm a biostatistician working in a lab where everyone else does both wet and dry lab research, and they all use benchling as their online lab notebook. Although I don't have much first hand experience using that website, they like having similar tools to what you describe in the browser like Sanger, being able to run multiple sequence alignment, manage lab inventory, etc.

A second question I have is I think it's great to simplify and integrate complex tasks in molecular biology but I'm curious about where one philosophically draws the line for scientific commercial products between ease of use and scientific reproducibility and transparency where such tools were not available or affordable in poorer countries.

It's OK to ask about competitors. I am not overly familiar with Benchling, my understanding is that is a lab notebook that offers some of the basic molecular biology sequence analysis tools, but not for genomics or protein. It is cloud based, so we've had some customers report lag issues that made daily use a chore. However, despite the limited toolsets and possible lag, I think it is generally well liked by their customers. And while free for academics, Benchling is one of the highest priced notebooks for commercial companies. DNASTAR provides the most robust solutions for Sanger data handling, so if you generate trace data frequently, you will want the best possible software.

Not sure I follow your second question?

Who’s your favorite Star Wars character?

the Toydarian parts dealer.

Specifically Watto or any Toydarian?

Anyone resistant to Jedi mind tricks...

Do you consider a hot dog a sandwich?

No, a hotdog is not a sandwich.

Can I borrow 50 bucks?

no.